WISP polypeptides and nucleic acids encoding same

ABSTRACT

Wnt-1-Induced Secreted Proteins (WISPs) are provided, whose genes are induced at least by Wnt-1. Also provided are nucleic acid molecules encoding those polypeptides, as well as vectors and host cells comprising those nucleic acid sequences, chimeric polypeptide molecules comprising the polypeptides fused to heterologous polypeptide sequences, antibodies which bind to the polypeptides, and methods for producing the polypeptides.

RELATED APPLICATIONS

This is a divisional application of U.S. patent application Ser. No. 10/112,267, filed on Mar. 27, 2002, now U.S. Pat. No. 7,101,850, which is a divisional application of U.S. patent application Ser. No. 09/182,145, filed on Oct. 29, 1998, now U.S. Pat. No. 6,387,657, which claims priority to U.S. Provisional Patent Application Ser. No. 60/063,704, filed Oct. 29, 1997, and to U.S. Provisional Patent Application Ser. No. 60/081,695, filed on Apr. 14, 1998, and to U.S. Provisional Patent Application Ser. No. 60/073,612, filed Feb. 4, 1998, the entire disclosures of which applications are hereby incorporated by reference.

GOVERNMENT LICENSE RIGHTS

This invention was made with government support under grant no. 5P01 CA41086, awarded by the National Institutes of Health, National Cancer Institute. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates generally to the identification and isolation of novel DNA and to the recombinant production of novel polypeptides having homology to connective tissue growth factor, designated herein as Wnt-1-Induced Secreted Proteins (WISPs).

BACKGROUND OF THE INVENTION

Malignant tumors (cancers) are the second leading cause of death in the United States, after heart disease. Boring et al., CA Cancer J. Clin., 43:7 (1993).

Cancer is characterized by the increase in the number of abnormal, or neoplastic, cells derived from a normal tissue which proliferate to form a tumor mass, the invasion of adjacent tissues by these neoplastic tumor cells, and the generation of malignant cells which eventually spread via the blood or lymphatic system to regional lymph nodes and to distant sites (metastasis). In a cancerous state a cell proliferates under conditions in which normal cells would not grow. Cancer manifests itself in a wide variety of forms, characterized by different degrees of invasiveness and aggressiveness.

Alteration of gene expression is intimately related to the uncontrolled cell growth and de-differentiation which are a common feature of all cancers.

The genomes of certain well studied tumors have been found to show decreased expression of recessive genes, usually referred to as tumor suppression genes, which would normally function to prevent malignant cell growth, and/or overexpression of certain dominant genes, such as oncogenes, that act to promote malignant growth. Each of these genetic changes appears to be responsible for importing some of the traits that, in aggregate, represent the full neoplastic phenotype. Hunter, Cell, 64:1129 (1991); Bishop, Cell, 64:35-248 (1991).

A well-known mechanism of gene (e.g., oncogene) overexpression in cancer cells is gene amplification. This is a process where in the chromosome of the ancestral cell multiple copies of a particular gene are produced. The process involves unscheduled replication of the region of chromosome comprising the gene, followed by recombination of the replicated segments back into the chromosome. Alitalo et al., Adv. Cancer Res., 47:235-281 (1986). It is believed that the overexpression of the gene parallels gene amplification, i.e., is proportionate to the number of copies made.

Proto-oncogenes that encode growth factors and growth factor receptors have been identified to play important roles in the pathogenesis of various human malignancies, including breast cancer. For example, it has been found that the human ErbB2 gene (erbB2, also known as her2, or c-erbB-2), which encodes a 185-kd transmembrane glycoprotein receptor (p185^(HER2); HER2) related to the epidermal growth factor receptor (EGFR), is overexpressed in about 25% to 30% of human breast cancer. Slamon et al., Science, 235:177-182 (1987); Slamon et al., Science, 244:707-712 (1989). It has been reported that gene amplification of a protooncogen is an event typically involved in the more malignant forms of cancer, and could act as a predictor of clinical outcome. Schwab et al., Genes Chromosomes Cancer, 1:181-193 (1990); Alitalo et al., supra. Thus, erbB2 overexpression is commonly regarded as a predictor of a poor prognosis, especially in patients with primary disease that involves axillary lymph nodes (Slamon et al., (1987) and (1989), supra; Ravdin and Chamness, Gene, 159:19-27 (1995); and Hynes and Stern, Biochim Biophys Acta, 1198:165-184 (1994)), and has been linked to sensitivity and/or resistance to hormone therapy and chemotherapeutic regimens, including CMF (cyclophosphamide, methotrexate, and fluoruracil) and anthracyclines. Baselga et al., Oncology, 11(3 Suppl 1):43-48 (1997). However, despite the association of erbB2 overexpression with poor prognosis, the odds of HER2-positive patients responding clinically to treatment with taxanes were greater than three times those of HER2-negative patients. Baselga et al., supra. A recombinant humanized anti-ErbB2 (anti-HER2) monoclonal antibody (a humanized version of the murine anti-ErbB2 antibody 4D5, referred to as rhuMAb HER2 or HERCEPTIN®) has been clinically active in patients with ErbB2-overexpressing metastatic breast cancers that had received extensive prior anticancer therapy. Baselga et al., J. Clin. Oncol., 14:737-744 (1996).

Cytokines have been implicated in the pathogenesis of a number of brain diseases in which neurological dysfunction has been attributed to a change in amino acid neurotransmitter metabolism. In particular, members of the transforming growth factor-β (TGF-β) family have been implicated. TGF peptides are small polypeptides that were first identified by their ability to induce proliferation and transformation in noncancerous cells in culture. Although initially defined as a growth factor, TGF-β also inhibits proliferation of epithelial, endothelial, lymphoid, and hematopoietic cells. This cytokine is thought to play an important role in regulating the duration of the inflammatory response, allowing the healing process to proceed. It is also a potent immunomodulator, which has many pleiotrophic effects, including regulating many other cytokines.

The TGF-β superfamily includes bone morphogenetic proteins (BMP-2, BMP-4, BMP-5, BMP-6, BMP-7), activins A & B, decapentaplegic (dpp), 60A, OP-2, dorsalin, growth differentiation factors (GDFs), nodal, MIS, Inhibin-∀, TGF-β1, TGF-β2, TGF-β3, TGF-β5, and glial-derived neurotrophic factor (GDNF). Atrisano, et al., J. Biochemica et Biophysica Acta, 1222:71-80 (1994), of particular interest are the growth differentiation factors, for as their name implies, these factors are implicated in the differentiation of cells.

Connective tissue growth factor (CTGF) is a growth factor induced in fibroblasts by many factors, including TGF-β and is essential for the ability of TGF-β to induce anchorage-independent growth (AIG), a property of transformed cells. CTGF was discovered in an attempt to identify the type of platelet derived growth factor (PDGF) dimers present in the growth media of cultured endothelial cells, and is related immunologically and biologically to PDGF. See U.S. Pat. No. 5,408,040. CTGF also is mitogenic and chemotactic for cells, and hence growth factors in this family are believed to play a role in the normal development, growth, and repair of human tissue.

Seven proteins related to CTGF, including the chicken ortholog for Cyr61, CEF10, human, mouse, and Xenopus laevis CTGF, and human, chicken, and Xenopus laevis Nov have been isolated, cloned, sequenced, and characterized as belonging to the CTGF gene family. Oemar and Luescher, Arterioscler. Thromb. Vasc. Biol., 17:1483-1489 (1997). The gene encoding Cyr61 has been found to promote angiogenesis, tumor growth, and vascularization. Babic et al., Proc. Natl. Acad. Sci. USA, 95:6355-6360 (1998). The nov gene is expressed in the kidney essentially at the embryonic stage, and alterations of nov expression, relative to the normal kidney, have been detected in both avian nephroblastomas and human Wilms' tumors. Martinerie et al., Oncogene, 9:2729-2732 (1994). Wt1 down regulates human nov expression, which down regulation might represent a key element in normal and tumoral nephrogenesis. Martinerie et al., Oncogene, 12:1479-1492 (1996). It has recently been proposed that the CTGF, nov, and cyr61 genes, which encode secreted proteins that contain conserved sequences and IGFBP motifs in their N-termini and bind IGFs with low affinity, represent more members of the IGFBP superfamily, along with the low-affinity mac25/IGFBP-7 (Yamanaka et al., J. Biol. Chem., 272:30729-30734 (1997)) and the high-affinity IGFBPs 1-6. CTGF under this proposal would be designated IGFBP-8. Kim et al., Proc. Natl., Acad. Sci. USA, 94:12981-12986 (1997).

Recently, a protein was found in the mouse designated ELM1 that is expressed in low metastatic cells. Hashimoto et al., J. Exp. Med., 187:289-296 (1998). The elm1 gene, a mouse homologue of WISP-1 disclosed below, is another member of the CTGF, Cyr61/Cef10, and neuroblastoma overexpressed-gene family and suppresses in vivo tumor growth and metastasis of K-1735 murine melanoma cells. Another recent article on rCop-1, the rat orthologue of WISP-2 described below describes the loss of expression of this gene after cell transformation. Zhang et al., Mol. Cell. Biol., 18:6131-6141 (1998).

CTGF family members (with the exception of nov) are immediate early growth-responsive genes that are thought to regulate cell proliferation, differentiation, embryo genesis, and wound healing. Sequence homology among members of the CTGF gene family is high; however, functions of these proteins in vitro range from growth stimulatory (i.e., human CTGF) to growth inhibitory (i.e., chicken Nov and also possibly hCTGF). Further, some molecules homologous to CTGF are indicated to be useful in the prevention of desmoplasia, the formation of highly cellular, excessive connective tissue stroma associated with some cancers, and fibrotic lesions associated with various skin disorders such as scleroderma, keloid, eosinophilic fasciitis, nodular fasciitis, and Dupuytren's contracture. Moreover, CTGF expression has recently been demonstrated in the fibrous stoma of mammary tumors, suggesting cancer stroma formation involves the induction of similar fibroproliferative growth factors as wound repair. Human CTGF is also expressed at very high levels in advanced atherosclerotic lesions, but not in normal arteries, suggesting it may play a role in atherosclerosis. Oemar and Luescher, supra. Therefore, molecules homologous to CTGF are of importance.

Extracellular and membrane-bound proteins play important roles in the formation, differentiation, and maintenance of multicellular organisms. The fate of many individual cells, e.g., proliferation, migration, differentiation, or interaction with other cells, is typically governed by information received from other cells and/or the immediate environment. This information is often transmitted by secreted polypeptides (for instance, mitogenic factors, survival factors, cytotoxic factors, differentiation factors, neuropeptides, and hormones), which are, in turn, received and interpreted by diverse cell receptors or membrane-bound proteins. These secreted polypeptides or signaling molecules normally pass through the cellular secretory pathway to reach their site of action in the extracellular environment, usually at a membrane-bound receptor protein.

Secreted proteins have various industrial applications, including use as pharmaceuticals, diagnostics, biosensors, and bioreactors. In fact, most protein drugs available at present, such as thrombolytic agents, interferons, interleukins, erythropoietins, colony stimulating factors, and various other cytokines, are secreted proteins. Their receptors, which are membrane-bound proteins, also have potential as therapeutic or diagnostic agents. Receptor immunoadhesins, for instance, can be employed as therapeutic agents to block receptor-ligand interaction. Membrane-bound proteins can also be employed for screening of potential peptide or small molecule inhibitors of the relevant receptor/ligand interaction. Such membrane-bound proteins and cell receptors include, but are not limited to, cytokine receptors, receptor kinases, receptor phosphatases, receptors involved in cell-cell interactions, and cellular adhesin molecules like selectins and integrins. Transduction of signals that regulate cell growth and differentiation is regulated in part by phosphorylation of various cellular proteins. Protein tyrosine kinases, enzymes that catalyze that process, can also act as growth factor receptors. Examples include fibroblast growth factor receptor and nerve growth factor receptor.

Efforts are being undertaken by both industry and academia to identify new, native secreted and membrane-bound receptor proteins, particularly those having homology to CTGF. Many efforts are focused on the screening of mammalian recombinant DNA libraries to identify the coding sequences for novel secreted and membrane-bound receptor proteins. Examples of screening methods and techniques are described in the literature. See, for example, Klein et al., Proc. Natl. Acad. Sci., 93:7108-7113 (1996); and U.S. Pat. No. 5,536,637.

Wnts are encoded by a large gene family whose members have been found in round worms, insects, cartilaginous fish, and vertebrates. Holland et al., Dev. Suppl., 125-133 (1994). Wnts are thought to function in a variety of developmental and physiological processes since many diverse species have multiple conserved Wnt genes. McMahon, Trends Genet., 8:236-242 (1992); Nusse and Varmus, Cell, 69:1073-1087 (1992). Wnt genes encode secreted glycoproteins that are thought to function as paracrine or autocrine signals active in several primitive cell types. McMahon, supra (1992); Nusse and Varmus, supra (1992). The Wnt growth factor family includes more than ten genes identified in the mouse (Wnt-1, -2, -3A, -3B, -4, -5A, -5B, -6, -7A, -7B, -8A, -8B, -10B, -11, -12, and -13) (see, e.g., Gavin et al., Genes Dev., 4:2319-2332 (1990); Lee et al., Proc. Natl. Acad. Sci. USA, 92:2268-2272 (1995); Christiansen et al., Mech. Dev., 51:341-350 (1995)) and at least nine genes identified in the human (Wnt-1, -2, -3, -5A, -7A, -7B, -8B, -10B, and -11) by cDNA cloning. See, e.g., Vant Veer et al., Mol. Cell. Biol., 4:2532-2534 (1984).

The Wnt-1 proto-oncogene (int-1) was originally identified from mammary tumors induced by mouse mammary tumor virus (MMTV) due to an insertion of viral DNA sequence. Nusse and Varmus, Cell, 31:99-109 (1982). In adult mice, the expression level of Wnt-1 mRNA is detected only in the testis during later stages of sperm development. Wnt-1 protein is about 42 KDa and contains an amino terminal hydrophobic region, which may function as a signal sequence for secretion (Nusse and Varmus, supra, 1992). The expression of WnL-2/irp is detected in mouse fetal and adult tissues and its distribution does not overlap with the expression pattern for Wnt-1. Wnt-3 is associated with mouse mammary tumorigenesis. The expression of Wnt-3 in Mouse embryos is detected in the neural tubes and in the limb buds. Wnt-5a transcripts are detected in the developing fore and hind limbs at 9.5 through 14.5 days and highest levels are concentrated in apical ectoderm at the distal tip of limbs. Nusse and Varmus, supra (1992). Recently, a Wnt growth factor, termed Wnt-x, was described (WO95/17416) along with the detection of Wnt-x expression in bone tissues and in bone-derived cells. Also described was the role of Wnt-x in the maintenance of mature osteoblasts and the use of the Wnt-x growth factor as a therapeutic agent or in the development of other therapeutic agents to treat bone-related diseases.

Wnts may play a role in local cell signaling. Biochemical studies have shown that much of the secreted Wnt protein can be found associated with the cell surface or extracellular matrix rather than freely diffusible in the medium. Papkoff and Schryver, Mol. Cell. Biol., 10:2723-2730 (1990); Bradley and Brown, EMBO J., 9:1569-1575 (1990).

Studies of mutations in Wnt genes have indicated a role for Wnts in growth control and tissue patterning. In Drosophila, wingless (wg) encodes a Wnt-related gene (Rijsewik et al., Cell, 50:649-657 (1987)) and wg mutations alter the pattern of embryonic ectoderm, neurogenesis, and imaginal disc outgrowth. Morata and Lawrence, Dev. Biol., 56:227-240 (1977); Baker, Dev. Biol., 125:96-108 (1988); Klingensmith and Nusse, Dev. Biol., 166:396-414 (1994). In Caenorhabditis elegans, lin-44 encodes a Wnt homolog which is required for asymmetric cell divisions. Herman and Horvitz, Development, 120:1035-1047 (1994). Knock-out mutations in mice have shown Wnts to be essential for brain development (McMahon and Bradley, Cell, 62:1073-1085 (1990); Thomas and Cappechi, Nature, 346:847-850 (1990)), and the outgrowth of embryonic primordia for kidney (Stark et al., Nature, 372:679-683 (1994)), tail bud (Takada et al., Genes Dev., 8:174-189 (1994)), and limb bud. Parr and McMahon, Nature, 374:350-353 (1995) Overexpression of Wnts in the mammary gland can result in mammary hyperplasia (McMahon, supra (1992); Nusse and Varmus, supra (1992)), and precocious alveolar development. Bradbury et al., Dev. Biol., 170:553-563 (1995).

Wnt-5a and Wnt-5b are expressed in the posterior and lateral mesoderm and the extraembryonic mesoderm of the day 7-8 murine embryo. Gavin et al., supra (1990). These embryonic domains contribute to the AGM region and yolk sac tissues from which multipotent hematopoietic precursors and HSCs are derived. Dzierzak and Medvinsky, Trends Genet., 11:359-366 (1995); Zon et al., in Gluckman and Coulombel, ed., Colloque, INSERM, 235:17-22 (1995), presented at the Joint International Workshop on Foetal and Neonatal Hematopoiesis and Mechanism of Bone Marrow Failure, Paris France, Apr. 3-6, 1995; Kanatsu and Nishikawa, Development, 122:823-830 (1996). Wnt-5a, Wnt-10b, and other Wnts have been detected in limb buds, indicating possible roles in the development and patterning of the early bone microenvironment as shown for Wnt-7b. Gavin et al., supra (1990); Christiansen et al., Mech. Devel., 51:341-350 (1995); Parr and McMahon, supra (1995).

The Wnt/Wg signal transduction pathway plays an important role in the biological development of the organism and has been implicated in several human cancers. This pathway also includes the tumor suppressor gene, APC. Mutations in the APC gene are associated with the development of sporadic and inherited forms of human colorectal cancer. The Wnt/Wg signal leads to the accumulation of beta-catenin/Armadillo in the cell, resulting in the formation of a bipartite transcription complex consisting of beta-catenin and a member of the lymphoid enhancer binding factor/T cell factor (LEF/TCF)HMG box transcription factor family. This complex translocates to the nucleus where it can activate expression of genes downstream of the Wnt/Wg signal, such as the engrailed and Ultrabithorax genes in Drosophila. The downstream target genes of Wnt-1 signaling in vertebrates that presumably function in tumorigenesis, however, are currently unknown.

For a most recent review on Wnt, see Cadigan and Nusse, Genes & Dev., 11:3286-3305 (1997).

There is a need to elucidate the further members of the above families, including cell-surface molecules that may be tumor-specific antigens or proteins that serve a regulatory function in initiating the Wnt pathway of tumorigenesis. These would also include downstream components of the Wnt signaling pathway that are important to the transformed phenotype and the development of cancer.

SUMMARY OF THE INVENTION

Several putative Wnt-1-induced genes have been identified at the mRNA level in a high-throughput cDNA substraction experiment. Thus, applicants have identified novel cDNA clones (WISP1, WISP2, and WISP3) that encode novel polypeptides of the WISP family, designated as WISP-1, WISP-2, and WISP-3, respectively. This class of polypeptides was formerly referred to as Wnt-1-induced Gene (WIG) polypeptides, with WISP-1 and WISP-2 formerly designated as WIG-1 and WIG-2, respectively. One of the cDNA clones encodes a novel polypeptide, human WISP-2, having homology to CTGF, wherein the polypeptide is designated in the present application as “human WISP-2” or “PR0261”. The WISP-1 and WISP-3 molecules also have homology to CTGF.

In one embodiment, this invention provides isolated nucleic acid comprising DNA having at least about 600 nucleotides and at least about a 75% sequence identity to (a) a DNA molecule encoding a human WISP-1 polypeptide comprising the sequence of amino acids 23 to 367 of FIGS. 3A-3C (SEQ ID NO:3), or (b) the complement of the DNA molecule of (a). Preferably, this nucleic acid has at least one WISP biological activity. In a more preferred embodiment, this nucleic acid has at least about a 95% sequence identity to (a) a DNA molecule encoding a human WISP-1 polypeptide comprising the sequence of amino acids 23 to 367 of FIGS. 3A-3C (SEQ ID NO:3), or (b) the complement of the DNA molecule of (a).

More preferred is the nucleic acid comprising DNA encoding a human WISP-1 polypeptide having amino acid residues 23 to 367 of FIGS. 3A-3C (SEQ ID NO:3), or DNA encoding a human WISP-1 polypeptide having amino acid residues 1 to 367 of FIGS. 3A-3C (SEQ ID NO:4), or the complement of either of the encoding DNAs. Further preferred is this nucleic acid comprising DNA encoding a human WISP-1 polypeptide having amino acid residues 23 to 367 or 1 to 367 of FIGS. 3A-3C except for an isoleucine residue at position 184 rather than a valine residue or a serine residue at position 202 rather than an alanine residue (SEQ ID NOS:5-8, respectively). Further preferred also is this nucleic acid comprising DNA encoding a human WISP-1 polypeptide having amino acid residues 23 to 367 or 1 to 367 of FIGS. 3A-3C except for an isoleucine residue at position 184 rather than a valine residue and a serine residue at position 202 rather than an alanine residue (SEQ ID NOS:21-22, respectively).

Also preferred is this nucleic acid comprising DNA encoding a mouse WISP-1 polypeptide having amino acid residues 23 to 367 of FIGS. 1A-1B (SEQ ID NO:11), or DNA encoding a mouse WISP-1 polypeptide having amino acid residues 1 to 367 of FIGS. 1A-1B (SEQ ID NO:12), or the complement of either of the encoding DNAs.

Also provided by this invention is isolated nucleic acid comprising DNA having at least about 600 nucleotides and at least about a 85% sequence identity to (a) a DNA molecule encoding a mouse WISP-1 polypeptide comprising the sequence of amino acids 23 to 367 of FIGS. 1A-1B (SEQ ID NO:11), or (b) the complement of the DNA molecule of (a). Preferably, this nucleic acid has at least one WISP biological activity. More preferably, this nucleic acid comprises DNA having at least about a 95% sequence identity to (a) a DNA molecule encoding a mouse WISP-1 polypeptide comprising the sequence of amino acids 23 to 367 of FIGS. 1A-1B (SEQ ID NO:11), or (b) the complement of the DNA molecule of (a).

In another preferred embodiment, the invention provides an isolated nucleic acid comprising DNA having at least about 600 nucleotides and at least about a 75% sequence identity to (a) a DNA molecule encoding the same full-length polypeptide encoded by the human WISP-1 polypeptide cDNA in ATCC Deposit No. 209533 (pRK5E.h.WISP-1.568.38), or (b) the complement of the DNA molecule of (a). This nucleic acid preferably comprises DNA having at least about 600 nucleotides and at least about a 95% sequence identity to (a) a DNA molecule encoding the same full-length polypeptide encoded by the human WISP-1 polypeptide cDNA in ATCC Deposit No. 209533 (pRK5E.h.WISP-1.568.38), or (b) the complement of the DNA molecule of (a).

In another aspect, the invention provides a process for producing a WISP-1 polypeptide comprising culturing a host cell comprising the above nucleic acid under conditions suitable for expression of the WISP-1 polypeptide and recovering the WISP-1 polypeptide from the cell culture. Additionally provided is an isolated WISP-1 polypeptide encoded by the above nucleic acid, including where the polypeptide is human WISP-1 or mouse WISP-1.

In another embodiment, the invention provides isolated nucleic acid comprising SEQ ID NO:23, 24, 25, 26, 27, 28, or 29, and an isolated WISP-1 polypeptide encoded by such a nucleic acid.

Also provided by this invention is an isolated nucleic acid having at least about 600 nucleotides and produced by hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a human WISP-1 polypeptide comprising the sequence of amino acids 23 to 367 of FIGS. 3A-3C (SEQ ID NO:3), or (b) the complement of the DNA molecule of (a), and, if the test DNA molecule has at least about a 75% sequence identity to (a) or (b), isolating the test DNA molecule.

Further provided is a polypeptide produced by (i) hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a human WISP-1 polypeptide comprising the sequence of amino acids 23 to 367 of FIGS. 3A-3C (SEQ ID NO:3), or (b) the complement of the DNA molecule of (a), and if the test DNA molecule has at least about a 75% sequence identity to (a) or (b), (ii) culturing a host cell comprising the test DNA molecule under conditions suitable for expression of the polypeptide, and (iii) recovering the polypeptide from the cell culture.

In another aspect, the invention provides isolated nucleic acid comprising DNA having at least about an 80% sequence identity to (a) a DNA molecule encoding a human WISP-2 polypeptide comprising the sequence of amino acids 24 to 250 of FIGS. 4A-4B (SEQ ID NO:15), or (b) the complement of the DNA molecule of (a). Preferably, this nucleic acid has at least one WISP biological activity. Also, preferably this nucleic acid comprises DNA having at least about a 95% sequence identity to (a) a DNA molecule encoding a human WISP-2 polypeptide comprising the sequence of amino acids 24 to 250 of FIGS. 4A-4B (SEQ ID NO:15), or (b) the complement of the DNA molecule of (a) In another preferred embodiment, this nucleic acid comprises DNA encoding a human WISP-2 polypeptide having amino acid residues 24 to 250 of FIGS. 4A-4B (SEQ ID NO:15), or DNA encoding a human WISP-2 polypeptide having amino acid residues 1 to 250 of FIGS. 4A-4B (SEQ ID NO:16), or a complement of either of the encoding DNAs.

In another aspect, the invention provides isolated nucleic acid comprising DNA having at least about an 80% sequence identity to (a) a DNA molecule encoding a human WISP-2 polypeptide comprising the sequence of amino acids 1 to 250 of FIGS. 4A-4B (SEQ ID NO:16), or (b) the complement of the DNA molecule of (a).

In another aspect, the invention provides isolated nucleic acid comprising DNA having at least about 500 nucleotides and at least about an 80% sequence identity to (a) a DNA molecule encoding a mouse WISP-2 polypeptide comprising the sequence of amino acids 24 to 251 of FIGS. 2A-2B (SEQ ID NO:19), or (b) the complement of the DNA molecule of (a). In a preferred embodiment, this nucleic acid comprises DNA having at least about a 95% sequence identity to (a) a DNA molecule encoding a mouse WISP-2 polypeptide comprising the sequence of amino acids 24 to 251 of FIGS. 2A-2B (SEQ ID NO:19), or (b) the complement of the DNA molecule of (a). More preferably, the nucleic acid comprises DNA encoding a mouse WISP-2 polypeptide having amino acid residues 24 to 251 of FIGS. 2A-2B (SEQ ID NO:19), or DNA encoding a mouse WISP-2 polypeptide having amino acid residues 1 to 251 of FIGS. 2A-2B (SEQ ID NO:20), or the complement of either of these encoding DNAs.

In a further aspect, the invention provides isolated nucleic acid comprising DNA having at least about 500 nucleotides and at least about an 80% sequence identity to (a) a DNA molecule encoding a mouse WISP-2 polypeptide comprising the sequence of amino acids 1 to 251 of FIGS. 2A-2B (SEQ ID NO:20), or (b) the complement of the DNA molecule of (a).

In yet another aspect, the invention provides an isolated nucleic acid comprising DNA having at least about 400 nucleotides and at least about a 75% sequence identity to (a) a DNA molecule encoding the same full-length polypeptide encoded by the human WISP-2 polypeptide cDNA in ATCC Deposit No. 209391 (DNA33473), or (b) the complement of the DNA molecule of (a). Preferably, this nucleic acid comprises DNA having at least about a 95% sequence identity to (a) a DNA molecule encoding the same full-length polypeptide encoded by the human WISP-2 polypeptide cDNA in ATCC Deposit No. 209391 (DNA33473), or (b) the complement of the DNA molecule of (a).

In another embodiment, this invention provides an isolated nucleic acid comprising the nucleotide sequence of the full-length coding sequence of clone UNQ228 (DNA33473) deposited under accession number ATCC 209391.

In another aspect, the invention provides a process for producing a WISP-2 polypeptide comprising culturing a host cell comprising the above nucleic acid under conditions suitable for expression of the WISP-2 polypeptide and recovering the WISP-2 polypeptide from the cell culture. Additionally provided is a WISP-2 polypeptide encoded by the isolated nucleic acid, including where the polypeptide is human WISP-2 or mouse WISP-2. In a specific embodiment of this, the invention provides isolated native-sequence human WISP-2 polypeptide comprising amino acid residues 1 to 250 of FIGS. 4A-4B (SEQ ID NO:16) or comprising amino acid residues 24 to 250 of FIGS. 4A-4B (SEQ ID NO:15).

In a further embodiment, the invention provides an isolated nucleic acid having at least about 400 nucleotides and produced by hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a human WISP-2 polypeptide comprising the sequence of amino acids 24 to 250 of FIGS. 4A-4B (SEQ ID NO:15), or (b) the complement of the DNA molecule of (a), and, if the test DNA molecule has at least about a 75% sequence identity to (a) or (b), isolating the test DNA molecule.

In a still further embodiment, the invention provides a polypeptide produced by (i) hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a human WISP-2 polypeptide comprising the sequence of amino acids 24 to 250 of FIGS. 4A-4B (SEQ ID NO:15), or (b) the complement of the DNA molecule of (a), and if the test DNA molecule has at least about a 75% sequence identity to (a) or (b), (ii) culturing a host cell comprising the test DNA molecule under conditions suitable for expression of the polypeptide, and (iii) recovering the polypeptide from the cell culture.

In yet another embodiment, the invention provides isolated nucleic acid comprising DNA having a 100% sequence identity in more than about 500 nucleotides to (a) a DNA molecule encoding a human WISP-3 polypeptide comprising the sequence of amino acids 34 to 372 of FIGS. 6A-6C (SEQ ID NO:32), or (b) the complement of the DNA molecule of (a). Preferably, this nucleic acid has at least one WISP biological activity. Preferably, this nucleic acid comprises DNA encoding a human WISP-3 polypeptide having amino acid residues 34 to 372 of FIGS. 6A-6C (SEQ ID NO:32) or amino acids 1 to 372 of FIGS. 6A-6C (SEQ ID NO:33), or the complement thereof.

In a still further, embodiment, the invention provides an isolated nucleic acid comprising DNA having a 100% sequence identity in more than about 500 nucleotides to (a) a DNA molecule encoding the same full-length polypeptide encoded by the human WISP-3 polypeptide cDNA in ATCC Deposit No. 209706 (DNA56350-1176-2), or (b) the complement of the DNA molecule of (a). A still further aspect of the invention involves a process for producing a WISP-3 polypeptide comprising culturing a host cell comprising WISP-3-encoding nucleic acid under conditions suitable for expression of the WISP-3 polypeptide and recovering the WISP-3 polypeptide from the cell culture.

Further provided is an isolated WISP-3 polypeptide encoded by the WISP-3-encoding nucleic acid. Preferably, this polypeptide is human WISP-3.

In another embodiment, the invention provides an isolated nucleic acid produced by hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a human WISP-3 polypeptide comprising the sequence of amino acids 34 to 372 of FIGS. 6A-6C (SEQ ID NO:32), or (b) the complement of the DNA molecule of (a), and, if the test DNA molecule has a 100% sequence identity to (a) or (b) in more than about 500 nucleotides, isolating the test DNA molecule.

Also provided is a polypeptide produced by (i) hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a human WISP-3 polypeptide comprising the sequence of amino acids 34 to 372 of FIGS. 6A-6C (SEQ ID NO:32), or (b) the complement of the DNA molecule of (a), and if the test DNA molecule has a 100% sequence identity to (a) or (b) in more than about 500 nucleotides, (ii) culturing a host cell comprising the test DNA molecule under conditions suitable for expression of the polypeptide, and (iii) recovering the polypeptide from the cell culture.

In yet another embodiment, the invention provides isolated nucleic acid comprising DNA having a 100% sequence identity in more than about 400 nucleotides to (a) a DNA molecule encoding a human WISP-3 polypeptide comprising the sequence of amino acids 16 to 355 of FIGS. 7A-7C (SEQ ID NO:36), or (b) the complement of the DNA molecule of (a). Preferably, this nucleic acid has at least one WISP biological activity. Preferably, this nucleic acid comprises DNA encoding a human WISP-3 polypeptide having amino acid residues 16 to 355 of FIGS. 7A-7C (SEQ ID NO:36), or amino acid residues 1 to 355 of FIGS. 7A-7C (SEQ ID NO:37) or the complement thereof.

In a still further embodiment, the invention provides an isolated nucleic acid comprising DNA having a 100% sequence identity in more than about 400 nucleotides to (a) a DNA molecule encoding the same full-length polypeptide encoded by the human WISP-3 polypeptide cDNA in ATCC Deposit No. 209707 (DNA58800-1176-2), or (b) the complement of the DNA molecule of (a).

A still further aspect of the invention involves a process for producing a WISP-3 polypeptide of FIG. 7A-7C comprising culturing a host cell comprising WISP-3-encoding nucleic acid under conditions suitable for expression of the WISP-3 polypeptide and recovering the WISP-3 polypeptide from the cell culture.

Further provided is an isolated WISP-3 polypeptide of FIG. 7A-7C encoded by the WISP-3-encoding nucleic acid. Preferably, this polypeptide is human WISP-3.

In another embodiment, the invention provides an isolated nucleic acid produced by hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a human WISP-3 polypeptide comprising the sequence of amino acids 16 to 355 of FIGS. 7A-7C (SEQ ID NO:36), or (b) the complement of the DNA molecule of (a), and, if the test DNA molecule has a 100% sequence identity to (a) or (b) in more than about 400 nucleotides, isolating the test DNA molecule.

Also provided is a polypeptide produced by (i) hybridizing a test DNA molecule under stringent conditions with (a) a DNA molecule encoding a human WISP-3 polypeptide comprising the sequence of amino acids 16 to 355 of FIGS. 7A-7C (SEQ ID NO:36), or (b) the complement of the DNA molecule of (a), and if the test DNA molecule has a 100% sequence identity to (a) or (b) in more than about 400 nucleotides, (ii) culturing a host cell comprising the test DNA molecule under conditions suitable for expression of the polypeptide, and (iii) recovering the polypeptide from the cell culture.

Preferably the complements of the DNA molecules herein remain stably bound to the primary sequence under at least moderate, and optionally, under high stringency conditions. Also provided are vectors comprising the above nucleic acids, host cells comprising the vector, preferably wherein the cell is a Chinese hamster ovary (CHO) cell, an E. coli cell, a baculovirus-infected cell, or a yeast cell.

Additionally provided are a chimeric molecule comprising one of the above polypeptides or an inactivated variant thereof, fused to a heterologous amino acid sequence, wherein the heterologous amino acid sequence may be, for example, an epitope tag sequence, a polyamino acid such as poly-histidine, or an immunoglobulin constant region (Fc). Also provided is an antibody which specifically binds to one of the above polypeptides, wherein the antibody can be a monoclonal antibody.

Further provided are a composition comprising one of the above polypeptides and a carrier therefor, and a composition comprising an antagonist to one of the polypeptides and a carrier therefor. In one such embodiment, the invention provides a composition comprising a WISP-1, WISP-2, or WISP-3 polypeptide and a pharmaceutically acceptable carrier. Preferably, the polypeptide is a human polypeptide. Also, preferably, these compositions may also comprise a chemotherapeutic agent or growth-inhibitory agent.

In another aspect, the invention provides a pharmaceutical product comprising:

(a) the composition comprising WISP-1, WISP-2, or WISP-3 polypeptide and a pharmaceutically acceptable carrier;

(b) a container containing said composition; and

(c) a label affixed to said container, or a package insert included in said pharmaceutical product referring to the use of said WISP-1, WISP-2, or WISP-3 polypeptide in the treatment of a WISP-related disorder.

In yet another embodiment, the invention provides a method for treating a WISP-related disorder in a mammal comprising administering to the mammal an effective amount of any of the above compositions, including the composition of a WISP-1, WISP-2, or WISP-3 polypeptide in a pharmaceutically acceptable carrier, and including the composition of an antagonist to a WISP-1, WISP-2, or WISP-3 polypeptide in a pharmaceutically acceptable carrier. Preferably, the disorder is a malignant disorder or arteriosclerosis. More preferably, the malignant disorder is breast cancer, ovarian cancer, colon cancer, or melanoma. Also, preferably the mammal is human. In another preferred embodiment, the WISP-1, WISP-2, or WISP-3 polypeptide is administered in combination with a chemotherapeutic agent, a growth inhibitory agent, or a cytotoxic agent.

In another embodiment, the invention supplies a process for diagnosing a disease or a susceptibility to a disease related to a mutation in a nucleic acid sequence encoding a WISP-1, WISP-2, or WISP-3 polypeptide comprising:

(a) isolating a nucleic acid sequence encoding a WISP-1, WISP-2, or WISP-3 polypeptide from a sample derived from a host; and

(b) determining a mutation in the nucleic acid sequence encoding a WISP-1, WISP-2, or WISP-3 polypeptide.

In another embodiment, the invention provides a method of diagnosing a WISP-related disorder in a mammal comprising detecting the level of expression of a gene encoding a WISP-1, WISP-2, or WISP-3 polypeptide (a) in a test sample of tissue cells obtained from the mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher or lower expression level in the test sample indicates the presence of a WISP-related dysfunction in the mammal from which the test tissue cells were obtained. Preferably, such a disorder is a type of cancer and a higher expression level in the test sample indicates the presence of a tumor in the mammal.

In a still further embodiment, the invention provides an isolated antibody binding a WISP-1, WISP-2, or WISP-3 polypeptide. Preferably, the antibody induces death of a cell overexpressing a WISP-1, WISP-2, or WISP-3 polypeptide, more preferably a cancer cell. Also preferred is an antibody that binds to a human WISP-1, WISP-2, or WISP-3 polypeptide, and is a human or humanized antibody. More preferred is a monoclonal antibody, still more preferred, a monoclonal antibody that has complementary-determining regions and constant immunoglobulin regions, and in other embodiments is an antibody fragment, a single-chain antibody, or an anti-idiotypic antibody. In addition, the antibody is suitably labeled with a detectable label or immobilized on a solid support.

Also provided is a composition comprising an antibody to a WISP-1, WISP-2, or WISP-3 polypeptide in admixture with a pharmaceutically acceptable carrier. Preferably, the antibody is to a human WISP-1, WISP-2, or WISP-3 polypeptide, and is a human or humanized antibody, most preferably a monoclonal antibody against human WISP-1. Further, the composition may comprise a growth-inhibitory amount of said antibody. In another embodiment, the invention provides a method for treating cancer in a mammal comprising administering to the mammal an effective amount of the above antibody composition. In a preferred aspect of this method, the cancer is colon cancer, the antibody is against human WISP-1 and is a humanized or human monoclonal antibody, and the mammal is human.

In another aspect, the invention provides a method for treating a WISP related disorder in a mammal comprising administering to the mammal an effective amount of a composition comprising an antagonist to a WISP-1, WISP-2, or WISP-3 polypeptide in a pharmaceutically acceptable carrier.

In a further aspect, the invention provides a method for inhibiting the growth of tumor cells comprising exposing a cell that overexpresses a Wnt-1-induced gene to an effective amount of an antagonist that inhibits the expression or activity of a WISP-1, WISP-2, or WISP-3 polypeptide.

A further aspect entails a method for inhibiting the growth of tumor cells comprising exposing said cells to an effective amount of the composition with the growth-inhibiting amount of an anti-WISP-1, anti-WISP-2, or anti-WISP-3 antibody in admixture with the carrier. In a preferred aspect of this method, the tumor cells are colon cancer cells, the antibody is against human WISP-1 and is a humanized or human monoclonal antibody, and the mammal is human.

Also provided herein is a kit comprising one of the above WISP polypeptides or WISP antagonists, such as anti-WISP antibodies, and instructions for using the polypeptide or antagonist to detect or treat a WISP-related disorder, such as cancer induced by Wnt, one such preferred kit is a cancer diagnostic kit comprising an anti-WISP-1, anti-WISP-2, or anti-WISP-3 antibody and a carrier in suitable packaging. Preferably, this kit further comprises instructions for using said antibody to detect the WISP-1, WISP-2, or WISP-3 polypeptide.

Also provided is a method for inducing cell death comprising exposing a cell which is induced by Wnt to an effective amount of one of the above WISP polypeptides or WISP antagonists, such as anti-WISP antibodies. Preferably, such cell is a cancer cell. More preferably, the cell is in a mammal, more preferably a human. In addition, an effective amount of another chemotherapeutic antibody is used in the exposure of the cell, such as an anti-ErbB2 antibody. Further, optionally the method comprises exposing the cell to a chemotherapeutic agent, a growth-inhibitory agent, or radiation. Optionally, the cell is exposed to the growth-inhibitory agent prior to exposure to the antibody.

In a further aspect, the invention provides an article of manufacture, comprising:

a container;

a label on the container; and

a composition comprising an active agent contained within the container; wherein the composition is effective for inducing cell death or inhibiting the growth of tumor cells, the label on the container indicates that the composition can be used for treating conditions characterized by overinduction of Wnt or a WISP-related disorder or by overexpression of a WISP-1, WISP-2, or WISP-3 polypeptide, and the active agent in the composition is an antagonist to one of the polypeptides, that is, an agent that inhibits the expression and/or activity of the WISP-1, WISP-2, or WISP-3 polypeptide. Preferably, the active agent in such article of manufacture is an anti-WISP-1, anti-WISP-2, or anti-WISP-3 antibody, and the label on the container indicates that the composition can be used for treating a WISP-related disorder.

In another embodiment, the invention provides a process for identifying agonists to a WISP-1, WISP-2, or WISP-3 polypeptide comprising:

(a) contacting cells and a compound to be screened under conditions suitable for the stimulation of cell proliferation by the polypeptide; and

(b) measuring the proliferation of the cells to determine if the compound is an effective agonist.

Additionally, the invention provides an agonist to a WISP-1, WISP-2, or WISP-3 polypeptide identified by the above process.

Further, the invention provides a method for identifying a compound that inhibits the expression or activity of a WISP-1, WISP-2, or WISP-3 polypeptide, comprising contacting a candidate compound with a WISP-1, WISP-2, or WISP-3 polypeptide under conditions and for a time sufficient to allow the compound and polypeptide to interact. In a preferred embodiment, this method comprises the steps of:

(a) contacting cells and a compound to be screened in the presence of the WISP-1, WISP-2, or WISP-3 polypeptide under conditions suitable for the stimulation of cell proliferation by polypeptide; and (b) measuring the proliferation of the cells to determine if the compound is an effective antagonist.

Further, a compound identified by this method is provided.

In another aspect, this invention provides a compound that inhibits the expression or activity of a WISP-1, WISP-2, or WISP-3 polypeptide.

In another embodiment, the invention provides a method for determining the presence of a WISP-1, WISP-2, or WISP-3 polypeptide comprising exposing a cell suspected of containing the WISP-1, WISP-2, or WISP-3 polypeptide to an anti-WISP-1, anti-WISP-2, or anti-WISP-3 antibody and determining binding of said antibody to said cell.

In another preferred embodiment, the invention provides a method of diagnosing a WISP-related disorder in a mammal comprising (a) contacting an anti-WISP-1, anti-WISP-2, or anti-WISP-3 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between the anti-WISP-1, anti-WISP-2, or anti-WISP-3 antibody and the WISP-1, WISP-2, or WISP-3 polypeptide in the test sample. Preferably, said test sample is obtained from an individual suspected to have neoplastic cell growth or proliferation. Also, preferably the antibody is labeled with a detectable label and/or is immobilized on a solid support.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1B show the derived amino acid sequence of a native-sequence mouse WISP-1 protein from amino acids 1 to 367 (SEQ ID NO:12) and the nucleotide sequence (and complementary sequence) encoding the protein (SEQ ID NOS:9 and 10, respectively). There is a 1104-bp coding region and 584 bp of 3′ untranslated region. In the Figure, amino acids 1 through 22 form a putative signal sequence, amino acids 23 through 367 are the putative mature protein (SEQ ID NO:11), with amino acids 86 to 88, 143 to 145, 284 to 286, and 343 to 345 being potential glycosylation sites. Potential protein kinase C phosphorylation sites are at amino acids 43-45, 159-161, 235-237, 292-294, 295-297, and 345-347. Potential casein kinase II phosphorylation sites are at amino acids 44-47, 131-134, 145-148, and 358-361. Potential N-myristoylation sites are at amino acids 18-23, 72-77, 127-132, 149-154, 231-236, and 289-294. A potential amidation site, is at amino acids 269-272. A potential prokaryotic membrane lipoprotein lipid attachment site is at amino acids 113-123. A potential von Willebrand C1 domain is at amino acids 130-146. A potential thrombospondin 1 domain is at amino acids 223-237. A potential CT module is at amino acids 301-312. A potential IGF binding protein consensus site is at amino acids 72-80.

FIGS. 2A-2B show the derived amino acid sequence of a native-sequence mouse WISP-2 protein from amino acids 1 to 251 (SEQ ID NO:20) and the nucleotide sequence (and complementary sequence) encoding the protein (SEQ ID NOS:17 and 18, respectively) from a clone 1367.3. There are 756 bp of coding nucleotides and 722 bp of 3′ untranslated region. In the Figure, amino acids 1 through 23 form a putative signal sequence; amino acids 24 through 251 are the putative mature protein (SEQ ID NO:19). A potential N-glycosylation site is at amino acids 197-200. A potential glycosaminoglycan attachment site is at amino acids 85-88. Potential protein kinase C phosphorylation sites are at amino acids 85-87 and 112-114. Potential N-myristoylation sites are at amino acids 49-54, 81-86, 126-131, 210-215, and 245-250. A potential amidation site is at amino acids 103-106. A potential phospholipase A2 aspartic acid active site is at amino acids 120-130. A potential IGF binding protein consensus signature is at amino acids 49-64. A potential von Willebrand C1 domain is at amino acids 107-123. A potential thrombospondin 1 domain is at amino acids 202-216. A potential IGF binding protein consensus site is at amino acids 49-57.

FIGS. 3A-3C show the derived amino acid sequence of a native-sequence human WISP-1 protein from amino acids 1 to 367 (SEQ ID NO:4) and the nucleotide sequence (and complementary sequence) encoding the protein (SEQ ID NOS:1 and 2, respectively). There are 1104 bp of coding region in this human clone 568.38, and 1638 bp of 3′ untranslated region. In the Figure, amino acids 1 through 22 form a putative signal sequence, amino acids 23 through 367 are the putative mature protein (SEQ ID NO:3), with amino acids 85 to 87, 143 to 145, 284 to 286, and 343 to 345 being potential glycosylation sites. A potential cAMP- and cGMP-dependent protein kinase phosphorylation site is from amino acids 171 to 174; potential protein kinase C phosphorylation sites are at amino acids 43-45, 235-237, 292-294, and 345-347. Potential casein kinase II phosphorylation sites are at amino acids 30-33, 145-148, and 358-361. Potential N-myristoylation sites are at amino acids 72-77, 127-132, 149-154, 201-206, 231-236, 289-294, and 327-332. A potential amidation site is at amino acids 269-272. A potential prokaryotic membrane lipoprotein lipid attachment site is at amino acids 113-123. A potential von Willebrand C1 domain is at amino acids 130-146. A potential thrombospondin I domain is at amino acids 223-237. A potential CT (C-Terminal) module is at amino acids 301-312. A potential IGF binding protein consensus site is at amino acids 72-80.

FIGS. 4A-4B show the derived amino acid sequence of a native-sequence human WISP-2 protein from amino acids 1 to 250 (SEQ ID NO:16) and the nucleotide sequence (and complementary sequence) encoding the protein (SEQ ID NOS:13 and 14, respectively). The coding region is 753 bp and the 3′ untranslated region is 519 bp. The putative signal sequence is from amino acid residues 1 through 23 and the putative mature region is from 24 through 250 (SEQ ID NO:15). The clone designated herein as “UNQ228” and/or “DNA33473-seq min” (SEQ ID NO:38) begins at nucleotide 34 of SEQ ID NO:13. Potential protein kinase C phosphorylation sites are at amino acids 4-6, 118-120, and 227-229. A potential casein-kinase II phosphorylation site is at amino acids 98-101. A potential N-myristoylation site is at amino acids 3-8, 49-54, 81-86, 85-90, 126-131, 164-169, 166-171, 167-172, 183-188, and 209-214. A potential IGF binding protein consensus signature is at amino acids 49-64. A potential von Willebrand C1 domain is at amino acids 107-123. A potential thrombospondin 1 domain is at amino acids 2,01-215. A potential IGF binding protein consensus site is at amino acids 49-57.

FIG. 5 shows a 841-bp consensus nucleotide sequence designated “DNA30843” (SEQ ID NO:39) derived from the nucleotide sequences of twenty different expressed sequence tags from Incyte. When aligned with the other sequences, DNA30843 has 3 gaps. It has 441 bp orf (+I). DNA30843 was used to design probes for isolation of human WISP-2.

FIGS. 6A-6C show the derived amino acid sequence of a native-sequence human WISP-3 protein from amino acids 1 to 372 (SEQ ID NO:33) and the nucleotide sequence (and complementary sequence) encoding the protein (SEQ ID NOS:30 and 31, respectively). In the Figure, amino acids 1 through 33 form a putative signal sequence, amino acids 34 through 372 are the putative mature protein (SEQ ID NO:32), with amino acids 196 to 198 and 326 to 328 being potential glycosylation sites. Potential protein kinase C phosphorylation sites are at amino acids 209-211, 246-248, 277-279, 308-310, and 342-344. Potential casein kinase II phosphorylation sites are at amino acids 47-50, 254-257, and 293-296. Potential N-myristoylation sites are at amino acids 21-26, 89-94, 139-144, 166-171, 180-185, 185-190, 188-193, 242-247, and 302-307. A potential amidation site is at amino acids 188-191. Potential prokaryotic membrane lipoprotein lipid attachment sites are at amino acids 130-140 and 160-170. A potential IGF binding protein signature site is at amino acids 89-104. A potential IGF binding protein site (less stringent than prosite's) is at amino acids 89-97.

FIGS. 7A-7C show the derived amino acid sequence of a native-sequence human WISP-3 protein from amino acids 1 to 355 (SEQ ID NO:37) and the nucleotide sequence (and complementary sequence) encoding the protein (SEQ ID NOS:34 and 35, respectively). This protein is believed to be a splice variant of the nucleotide sequence shown in FIG. 6 with a shorter 5′ end. In the Figure, amino acids 1 through 15 form a putative signal sequence, amino acids 16 through 355 are the putative mature protein (SEQ ID NO:36), with amino acids 178 to 180 and 308 to 310 being potential glycosylation sites. Potential protein kinase C phosphorylation sites are at amino acids 191-193, 228-230, 259-261, 290-292, and 324-326. Potential casein kinase II phosphorylation sites are at amino acids 29-32, 236-239, and 275-278. Potential N-myristoylation sites are at amino acids 3-8, 71-76, 121-126, 148-153, 162-167, 167-172, 170-175, 224-229, and 284-289. A potential amidation site is at amino acids 170-173. Potential prokaryotic membrane lipoprotein lipid attachment sites are at amino acids 112-122 and 142-152. A potential IGF binding protein signature site is at amino acids 71-87. A potential IGF binding protein site (less stringent than prosite's) is at amino acids 71-79.

FIG. 8 shows an alignment of the full-length amino acid sequences of the human and mouse WISP-1 (SEQ ID NOS:4 and 12, respectively).

FIG. 9 shows an alignment of the full-length amino acid sequences of the human and mouse WISP-2 (SEQ ID NOS:16 and 20, respectively).

FIG. 10 shows an alignment of the amino acid sequences of the two clones of human WISP-3 (SEQ ID NOS:33 and 37, respectively).

FIG. 11A-11C show an alignment of the nucleotide sequences of human WISP-1 (nucleotides 89-1188 of SEQ ID NO:1) and the human WISP-3 (SEQ ID NO:30).

FIG. 12 shows an alignment of the amino acid sequences of human WISP-1 (SEQ ID NO:4) and the human WISP-3 (SEQ ID NO:33).

FIG. 13 shows a map of the vector pBabe puro (5.1 kb) used to transform cells for purposes of differential expression. The vector includes both unique restriction sites and multiple restriction sites. It is shown here in modified form for Wnt-1 cloning wherein the HindIII site after the SV40 promoter in the original pBabe puro vector has been removed and a HindIII site added to the multiple cloning site of the original pBabe puro vector. Wnt-1 is cloned from EcoRI-HindIII in the multiple cloning site. Constructs derived from this vector are selected in ampicillin (100 μg/ml) and the cells infected in culture are selected in 1.0-2.5 μg/ml puromycin.

FIG. 14 shows the sequences of the PCR-Select@ cDNA synthesis primer (SEQ ID NO:40), adaptors 1 and 2 (SEQ ID NOS:41 and 42, respectively) and complementary sequences for the adaptors (SEQ ID NOS:43 and 44, respectively), PCR primer 1 (SEQ ID NO:45), PCR primer 2 (SEQ ID NO:46), nested PCR primer 1 (SEQ ID NO:47), nested PCR primer 2 (SEQ ID NO:48), control primer G3PDH 51 primer (SEQ ID NO:49), and control primer G3PDH 3′ primer (SEQ ID NO:50) used for suppression subtractive hybridization for identifying WISP clones. When the adaptors are ligated to RsaI-digested cDNA, the RsaI site is restored.

FIG. 15 shows the cloning site region of the plasmid pGEM-T used to clone all of the WISP sequences herein (SEQ ID NOS:51 and 52 for 5′ and 3′ sequences, respectively).

FIGS. 16A-16D show the sequence (SEQ ID NO:53) of a plasmid that is used to prepare an expression plasmid for expression of mouse WISP-1 in mammalian cells, the latter being designated pRK5.CMV.puro-dhfR.mWISP-1.6His.

FIGS. 17A-17D show the sequence (SEQ ID NO:54) of plasmid pb.PH.IgG, which is used to prepare an expression plasmid for expression of mouse WISP-1 DNA in baculovirus-infected insect cells.

FIGS. 18A-18D show the sequence (SEQ ID NO:55) of plasmid pbPH.His.c, which is used to prepare an expression plasmid for expression of mouse WISP-1 DNA in baculovirus-infected insect cells, the latter being designated pbPH.mu.568.8his.baculo.

FIGS. 19A-19D show graphs of the delta CT in nine colon cancer cell lines and DNA from the blood of ten normal human donors (Nor Hu) as control, for human TNF, human WISP-1. Lyra, and human Apo2 ligand, respectively, using the ABI Prism 7700™ Sequence Detection System procedure for testing genomic amplification.

FIGS. 20A-20D show graphs of the delta CT in nine colon cancer cell lines and Nor Hu as control, for human DCR1, huFAS, human WISP-2, and Apo3, respectively, using the ABI Prism 7700™ Sequence Detection System procedure for testing genomic amplification.

FIGS. 21A-21D show graphs of the delta CT in nine colon cancer cell lines and Nor Hu as control, for three different runs of human WISP-1 (designated in the figure as huWISP-1c, -1b, and -1a) and the average of these three runs of human WISP-1, respectively, using the ABI Prism 7700™ Sequence Detect-Ion System procedure for testing genomic amplification.

FIGS. 22A-22D show graphs of the delta CT in nine colon cancer cell lines and Nor Hu as control, for three different runs of human WISP-2 (designated in the figure as huWISP-2c, -2b, and -2a; FIGS. 22A, C, and D, respectively) and the average of these three runs of human WISP-2 (FIG. 22B), using the ABI Prism 7700™ Sequence Detection System procedure for testing genomic amplification.

FIGS. 23A-23C show graphs of the delta CT in nine colon cancer cell lines and Nor Hu as control, for two different runs of human DR5 (DR5a and DR5b) and the average of these two runs of DR5, respectively, using the ABI Prism 7700™, Sequence Detection System procedure for testing genomic amplification.

FIGS. 24A-24D show graphs of the delta CT in nine colon cancer cell lines and Nor Hu as control, for four different runs of c-myc (c-myc(a1), c-myc(b1), c-myc (b), and c-myc (a)), respectively, using the ABI Prism 7700™ Sequence Detection System procedure for testing genomic amplification.

FIGS. 25A-25D show graphs of the delta CT in nine colon cancer cell lines and Nor Hu as control, for two different runs of human WISP-1 (designated in the figure as huWISP-1(a) and huWISP-1(b)) and for two different runs of human WISP-2 (designated in the figure as huWISP-2(a) and huWISP-2(b)), respectively, using the ABI Prism 7700™ Sequence Detection System procedure for testing genomic amplification.

FIG. 26 shows the sequence (SEQ ID NO:23) of clone 568.13, a potential splice variant of human WISP-1 obtained by screening with a probe derived from clone 568.15A, which is the initial clone isolated from a human lung library in the process to obtain full-length human WISP-1 DNA.

FIG. 27 shows the sequence (SEQ ID NO:24) of clone 568.1A, a potential human WISP-1 splice variant, 51 end only, obtained by screening with a probe derived from clone 568.15A.

FIG. 28 shows the sequence (SEQ ID NO:25) of clone 568.39, a potential human WISP-1 splice variant, 5′ end only, obtained by screening with a probe derived from clone 568.15A.

FIG. 29 shows the sequence (SEQ ID NO:26) of clone 568.4A, a potential human WISP-1 splice variant obtained by screening with a probe derived from clone 568.15A.

FIG. 30 shows the sequence (SEQ ID NO:27) of clone 568.5A, a potential human WISP-1 splice variant, 51 end only, obtained by screening with a probe derived from clone 568.15A.

FIG. 31 shows the sequence (SEQ ID NO:28) of clone 568.6B, a potential human WISP-1 splice variant, 51 end only, obtained by screening with a probe derived from clone 568.15A.

FIG. 32 shows the sequence (SEQ ID NO:29) of clone 568.7, a potential human WISP-1 splice variant, 51 end only, obtained by screening with a probe derived from clone 568.15A.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

I. Definitions

The term “WISP polypeptide” refers to the family of native-sequence human and mouse WISP proteins and variants described herein whose genes are induced at least by Wnt-1. This term includes WISP-1, WISP-2, and WISP-3.

The terms “WISP-1 polypeptide”, “WISP-1 homologue” and grammatical variants thereof, as used herein, encompass native-sequence WISP-1 protein and variants (which are further defined herein). The WISP-1 polypeptide may be isolated from a variety of sources, such as from human tissue types or from another source, or prepared by recombinant or synthetic methods, or by any combination of these and similar techniques.

The terms “WISP-2 polypeptide”, “WISP-2 homologue”, “PR0261”, and “PR0261 polypeptide” and grammatical variants thereof, as used herein, encompass native-sequence WISP-2 protein and variants (which are further defined herein). The WISP-2 polypeptide may be isolated from a variety of sources, such as from human tissue types or from another source, or prepared by recombinant or synthetic methods, or by any combination of these and similar techniques.

The terms “WISP-3 polypeptide”, “WISP-3 homologue”, and grammatical variants thereof, as used herein, encompass native-sequence WISP-3 protein and variants (which are further defined herein) The WISP-3 polypeptide may be isolated from a variety of sources, such as from human tissue types or from another source, or prepared by recombinant or synthetic methods, or by any combination of these and similar techniques.

A “native-sequence WISP-1 polypeptide” comprises a polypeptide having the same amino acid sequence as a WISP-1 polypeptide derived from nature. Such native-sequence WISP-1 polypeptides can be isolated from nature or can be produced by recombinant or synthetic means. The term “native-sequence WISP-1 polypeptide” specifically encompasses naturally occurring truncated or secreted forms of a WISP-1 polypeptide disclosed herein, naturally occurring variant forms (e.g., alternatively spliced forms or splice variants), and naturally occurring allelic variants of a WISP-1 polypeptide. In one embodiment of the invention, the native-sequence WISP-1 polypeptide is a mature or full-length native-sequence human WISP-1 polypeptide comprising amino acids 23 to 367 of FIGS. 3A-3C (SEQ ID NO: 3) or amino acids 1 to 367 of FIGS. 3A-3C (SEQ ID NO: 4), respectively, with or without the N-terminal methionine.

In another embodiment of the invention, the native-sequence WISP-1 polypeptide is the full-length or mature native-sequence human WISP-1 polypeptide comprising amino acids 23 to 367 or 1 to 367 of FIGS. 3A-3C wherein the valine residue at position 184 or the alanine residue at position 202 has/have been changed to an isoleucine or serine residue, respectively (SEQ ID NOS: 5-8), with or without the N-terminal methionine. In another embodiment of the invention, the native-sequence WISP-1 polypeptide is the full-length or mature native-sequence human WISP-1 polypeptide comprising amino acids 23 to 367 or 1 to 367 of FIGS. 3A-3C wherein the valine residue at position 184 and the alanine residue at position 202 has/have been changed to an isoleucine or serine residue, respectively (SEQ ID NOS: 21 and 22, respectively), with or without the N-terminal methionine. In another embodiment of the invention, the native sequence WISP-1 polypeptide is a mature or full-length native-sequence mouse WISP-1 polypeptide comprising amino acids 23 to 367 of FIGS. 1A-1B (SEQ ID NO: 11), or amino acids 1 to 367 of FIGS. 1A-1B (SEQ ID NO: 12), respectively, with or without the N-terminal methionine.

In another embodiment of the invention, the native-sequence WISP-1 polypeptide is one which is encoded by a nucleotide sequence comprising one of the human WISP-1 splice or other native-sequence variants, including SEQ ID NOS:23, 24, 25, 26, 27, 28, or 29, with or without an N-terminal methionine.

A “native-sequence WISP-2 polypeptide” or a “native-sequence PRO261 polypeptide” comprises a polypeptide having the same amino acid sequence as a WISP-2 polypeptide derived from nature. Such native-sequence WISP-2 polypeptides can be isolated from nature or can be produced by recombinant or synthetic means. The term “native-sequence WISP-2 polypeptide” specifically encompasses naturally occurring truncated or secreted forms of a WISP-2 polypeptide disclosed herein, naturally occurring variant forms (e.g., alternatively spliced forms or splice variants), and naturally occurring allelic variants of a WISP-2 polypeptide. In one embodiment of the invention, the native-sequence WISP-2 polypeptide is a mature or full-length native-sequence human WISP2 polypeptide comprising amino acids 1-24 up to 250 of FIGS. 4A-4B (SEQ ID NOS:15, 16, and 56-77), including amino acids 24 to 250 and amino acids 1 to 250 of FIGS. 4A-4B (SEQ ID NOS:15 and 16, respectively), with or without the N-terminal methionine. In another embodiment of the invention, the native-sequence WISP-2 polypeptide is a mature or full-length native-sequence mouse WISP-2 polypeptide comprising amino acids 1-24 up to 251 of FIGS. 2A-2B (SEQ ID NOS:19, 20, and 78-99), including amino acids 24 to 251 and amino acids 1 to 251 of FIGS. 2A-2B (SEQ ID NOS:19 and 20, respectively), with or without the N-terminal methionine.

A “native-sequence WISP-3 polypeptide” comprises a polypeptide having the same amino acid sequence as a WISP-3 polypeptide derived from nature. Such native-sequence WISP-3 polypeptides can be isolated from nature or can be produced by recombinant or synthetic means. The term “native-sequence WISP-3 polypeptide” specifically encompasses naturally occurring truncated or other forms of a WISP-3 polypeptide disclosed herein, naturally occurring variant forms (e.g., alternatively spliced forms or splice variants), and naturally occurring allelic variants of a WISP-3 polypeptide. In one embodiment of the invention, the native-sequence WISP-3 polypeptide is a mature or full-length, native-sequence human WISP-3 polypeptide comprising amino acids 34 to 372 of FIGS. 6A-6C (SEQ ID NO:32) or amino acids 1 to 372 of FIGS. 6A-6C (SEQ ID NO:33), respectively, with or without the N-terminal methionine. In another embodiment of the invention, the native-sequence WISP-3 polypeptide is a mature or full-length, native-sequence human WISP-3 polypeptide comprising amino acids 16 to 355 of FIGS. 7A-7C (SEQ ID NO:36) or amino acids 1 to 355 of FIGS. 7A-7C (SEQ ID NO:37) respectively, with or without the N-terminal methionine.

The term “WISP-1 variant” means an active WISP-1 polypeptide as defined below having at least about 80%, preferably at least about 85%, more preferably at least about 90%, most preferably at least about 95% amino acid sequence identity with human mature WISP-1 having the deduced amino acid sequence shown in FIGS. 3A-3C (SEQ ID NO: 3), and/or with human full-length WISP-1 having the deduced amino acid sequence shown in FIGS. 3A-3C (SEQ ID NO: 4), and/or with mouse mature WISP-1 having the deduced amino acid sequence shown in FIG. 1A-1B (SEQ ID NO: 11), and/or with mouse full-length WISP-1 having the deduced amino acid sequence shown in FIG. 1A-1B (SEQ ID NO: 12). Such variants include, for example, WISP-1 polypeptides wherein one or more amino acid residues are added to, or deleted from, the N- or C-terminus of the full-length or mature sequences of FIGS. 3A-3C and 1A-1B (SEQ ID NOS:4, 3, 12, and 11, respectively), including variants from other species, but excludes a native-sequence WISP-1 polypeptide.

The term “WISP-2 variant” or “PR0261 variant” means an active WISP-2 polypeptide as defined below having at least about 80%, preferably at least about 85%, more preferably at least about 90%, most preferably at least about 95% amino acid sequence identity with human mature WISP-2 having the putative deduced amino acid sequence shown in FIG. 4A-4B (SEQ ID NO:15), and/or with human full-length WISP-2 having the deduced amino acid sequence shown in FIG. 4A-4B (SEQ ID NO:16), and/or with mouse mature WISP-2 having the putative deduced amino acid sequence shown in FIG. 2A-2B (SEQ ID NO:19), and/or with mouse full-length WISP-2 having the deduced amino acid sequence shown in FIG. 2A-2B (SEQ ID NO:20).

Such variants include, for instance, WISP-2 polypeptides wherein one or more amino acid residues are added to, or deleted from, the N- or C-terminus of the full-length and putative mature sequences of FIGS. 4A-4B and 2A-2B (SEQ ID NOS:16, 15, 20, and 19, respectively), including variants from other species, but excludes a native-sequence WISP-2 polypeptide.

The term “WISP-3 variant” means an active WISP-3 polypeptide as defined below having at least about 80%, preferably at least about 85%, more preferably at least about 90%, most preferably at least about 95% amino acid sequence identity with human mature WISP-3 having the deduced amino acid sequence shown in FIGS. 6A-6C (SEQ ID NO:32), and/or with human full-length WISP-3 having the deduced amino acid sequence shown in FIGS. 6A-6C (SEQ ID NO:33), and/or with human mature WISP-3 having the deduced amino acid sequence shown in FIGS. 7A-7C (SEQ ID NO:36), or with human full-length WISP-3 having the deduced amino acid sequence shown in FIGS. 7A-7C (SEQ ID NO:37). Such variants include, for instance, WISP-3 polypeptides wherein one or more amino acid residues are added to, or deleted from, the N- or C-terminus of the full-length or mature sequences of FIGS. 6A-6C and 7A-7C (SEQ ID NOS:32, 33, 36, and 37, respectively), including variants from other species, but excludes a native-sequence WISP-3 polypeptide.

“Percent (%) amino acid sequence identity” with respect to the WISP sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in a WISP polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, ALIGN, or Megalign (DNASTAR™) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.

“Percent (%) nucleic acid sequence identity” with respect to the coding region of the WISP sequences identified herein, including UNQ228 (DNA34387-seq min) sequence, and the coding region therein, is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the coding region of the WISP sequence of interest, e.g., in the UNQ228 (DNA34387-seq min) sequence (SEQ ID NO:38) or coding region therein (SEQ ID NO:16), after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, ALIGN, or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.

“Stringent conditions” are those that (1) employ low ionic strength and high temperature for washing, for example, 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (vol/vol) formamide with 0.1%; bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mm sodium citrate at 42° C.; (3) employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8) 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC and 0.1% SDS; or (4) employ a buffer of 109 dextran sulfate, 2×SSC (sodium chloride/sodium citrate), and 50% formamide at 55° C., followed by a high-stringency wash consisting of 0.1×SSC containing EDTA at 55° C.

“Moderately stringent conditions” are described in Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989), and include the use of a washing solution and hybridization conditions (e.g., temperature, ionic strength, and percent SDS) less stringent than described above. An example of moderately stringent conditions is a condition such as overnight incubation at 370C. in a solution comprising: 20% formamide, 5×SSC (150 mM NaCl, is mm trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, lot dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA, followed by washing the filters in 1×SSC at about 37-50° C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc., as necessary to accommodate factors such as probe length and the like.

“Isolated,” when used to describe the various polypeptides disclosed herein, means polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In preferred embodiments, the polypeptide will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain. Isolated polypeptide includes polypeptide in situ within recombinant cells, since at least one component of the WISP natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step. An “isolated” nucleic acid encoding a WISP polypeptide or “isolated” DNA33473 or “isolated” PR0261 polypeptide-encoding nucleic acid molecule is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the respective nucleic acid. Isolated DNA33473 or an isolated WISP-encoding nucleic acid molecule is other than in the form or setting in which it is found in nature. An isolated WISP-encoding or DNA33473 nucleic acid molecule therefore is distinguished from the WISP-encoding or DNA33473 nucleic acid molecule, respectively, as it exists in natural cells. However, an isolated WISP-encoding or DNA33473 nucleic acid molecule includes a nucleic acid molecule contained in cells that ordinarily express WISP-encoding DNA or DNA33473, respectively, where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.

The term “control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.

Nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptides; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, “operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.

The term “antibody” is used in the broadest sense and specifically covers single anti-WISP polypeptide, such as anti-PR0261, monoclonal antibodies (including agonist, antagonist, and neutralizing antibodies), and anti-WISP polypeptide, such as anti-PR0261, and antibody compositions with polyepitopic specificity. The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts.

“Active” or “activity” or “WISP biological activity”, for purposes herein, describes form(s) of a WISP polypeptide, such as PR0261, including its variants, or its antagonists, which retain the biologic and/or immunologic activities of a native or naturally occurring (native-sequence) WISP polypeptide, such as PR0261, or its antagonist. Preferred “activities” for a WISP polypeptide or its antagonist include the ability to inhibit proliferation of tumor cells or to stimulate proliferation of normal cells and to treat arteriosclerosis, including atherosclerosis, as well as to induce wound repair and hematopoiesis, prevent desmoplasia, prevent fibrotic lesions associated with skin disorders such as scleroderma, keloid, eosinophilic fasciitis, nodular fasciitis, and Dupuytren's contracture, to treat bone-related diseases such as osteoporosis, to regulate anabolism including promotion of growth, to treat immune disorders, to treat Wilms' tumor and kidney-related disorders, to treat testis-related disorders, to treat lung-related disorders, and to treat cardiac disorders.

An “antagonist” of a WISP polypeptide is a molecule that inhibits an activity of a WISP polypeptide. Preferred antagonists are those which interfere with or block an undesirable biological activity of a WISP polypeptide, such as where a WISP polypeptide might act to stimulate cancer cells and the antagonist would serve to inhibit the growth of those cells. In some cases, such as with WISP-1, WISP-2, and WISP-3, the antagonist may be useful to inhibit the binding of a WISP polypeptide to an IGF. Such molecules include anti-bodies and small molecules that have such inhibitory capability, as well as WISP polypeptide variants of, and receptors for, WISP polypeptide (if available) or portions thereof that bind to WISP. For example, antagonists can be derived from receptors of WISP-1, WISP-2, and WISP-3 using the predicted family of receptors for WISPs-1, -2, and -3 (the CTGF receptors). Thus, the receptor can be expression cloned from the family; then a soluble form of the receptor is made by identifying the extracellular domain and excising the transmembrane domain therefrom. The soluble form of the receptor can then be used as an antagonist, or the receptor can be used to screen for small molecules that would antagonize WISP polypeptide activity.

Alternatively, using the murine sequences shown in FIGS. 1A-1B and 2A-2B (SEQ ID NOS:11, 12, 19, and 20, respectively) or the human sequences shown in FIGS. 3A-3C, 4A-4B, (SEQ ID NOS:3, 4, 15, and 16, respectively), 6A-6C, and 7A-7C, variants of native WISP-1, WISP-2, or WISP-3, are made that act as antagonists. Using knowledge from the CTGF receptor family, the receptor binding sites of WISP-1, WISP-2, and WISP-3 polypeptides can be determined by binding studies and one of them eliminated by standard techniques (deletion or radical substitution) so that the molecule acts as an antagonist.

Antagonist activity can be determined by several means, including standard assays for induction of cell death such as that described herein, e.g., ³H-thymidine proliferation assays, or other mitogenic assays, such as an assay measuring the capability of the candidate antagonist of inducing EGF-potentiated anchorage independent growth of target cell lines (Volckaert et al., Gene, 15:215-223 (1981)) and/or growth inhibition of neoplastic cell lines. Roberts et al., Proc. Natl. Acad. Sci. USA, 82:119-123 (1985). Anchorage-independent growth refers to the ability of WISP polypeptide-treated, or TGF-β-treated and EGF-treated non-neoplastic target cells to form colonies in soft agar, a characteristic ascribed to transformation of the cells. In this assay, the candidate is incubated together with an equimolar amount of a WISP polypeptide otherwise detectable in the EGF-potentiated anchorage-independent target cell growth assay, and the culture observed for failure to induce anchorage independent growth. In addition, an antagonist may be an IGF such as IGF-I or a peptide mimic of IGF-I or a receptor to IGF or a receptor to an IGFBP.

“Treatment” refers to both therapeutic treatment and prophylactic or preventative measures. Those in need of treatment include those already with the disorder or condition as well as those in which the disorder or condition is to be prevented.

“Mammal” for purposes of treatment refers to any animal classified as a mammal, including humans, domestic, and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, sheep, pigs, cows, etc. Preferably, the mammal is human.

A “disorder” or “WISP-related disorder” is any condition that would benefit from treatment with the WISP polypeptides or WISP antagonists herein. This includes chronic and acute disorders, as well as those pathological conditions which predispose the mammal to the disorder in question. Non-limiting examples of disorders to be treated herein include benign and malignant tumors; leukemias and lymphoid malignancies; neuronal, glial, astrocytal, hypothalamic and other glandular, macrophagal, epithelial, stromal, and blastocoelic disorders; hematopoiesis-related disorders; tissue-growth disorders; skin disorders; desmoplasia, fibrotic lesions; kidney disorders; bone-related disorders; trauma such as bums, incisions, and other wounds; catabolic states; testicular-related disorders; and inflammatory, angiogenic, and immunologic disorders, including arteriosclerosis. A “Wnt-related disorder” is one caused at least by the upregulation of the Wnt gene pathway, including Wnt-1 and Wnt-4, but preferably Wnt-1, and may include cancer.

The terms “cancer”, “cancerous”, and “malignant” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. Examples of cancer include but are not limited to, carcinoma including adenocarcinoma, lymphoma, blastoma, melanoma, sarcoma, and leukemia. More particular examples of such cancers include squamous cell cancer, small-cell lung cancer, non-small cell lung cancer, gastrointestinal cancer, Hodgkin's and non-Hodgkin's lymphoma, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer such as hepatic carcinoma and hepatoma, bladder cancer, breast cancer, colon cancer, colorectal cancer, endometriat carcinoma, salivary gland carcinoma, kidney cancer such as renal cell carcinoma and Wilms' tumors, basal cell carcinoma, melanoma, prostate cancer, vulval cancer, thyroid cancer, testicular cancer, esophageal cancer, and various types of head and neck cancer. The preferred cancers for treatment herein are breast, colon, lung, and melanoma.

The term “cytotoxic agent” as used herein refers to a substance that inhibits or prevents the function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes (e.g., ¹³¹I, ¹²⁵I, ⁹⁰Y, and ¹⁸⁶Re), chemotherapeutic agents, and toxins such as enzymatically active toxins of bacterial, fungal, plant, or animal origin, or fragments thereof.

A “chemotherapeutic agent” is a chemical compound useful in the treatment of cancer. Examples of chemotherapeutic agents include Adriamycin, Doxorubicin, 5-Fluorouracil, Cytosine arabinoside (“Ara-C”), Cyclophosphamide, Thiotepa, Busulfan, Cytoxin, Taxol, Toxotere, Methotrexate, Cisplatin, Melphalan, Vinblastine, Bleomycin, Etoposide, Ifosfamide, Mitomycin C, Mitoxantrone, Vincreistine, Vinorelbine, Carboplatin, Teniposide, Daunomycin, Carminomycin, Aminopterin, Dactinomycin, Mitomycins, Esperamicins (see U.S. Pat. No. 4,675,187), Melphalan, and other related nitrogen mustards. Also included in this definition are hormonal agents that act to regulate or inhibit hormone action on tumors, such as tamoxifen and onapristone.

A “growth-inhibitory agent” when used herein refers to a compound or composition which inhibits growth of a cell, such as an Wnt-overexpressing cancer cell, either in vitro or in vivo. Thus, the growth-inhibitory agent is one which significantly reduces the percentage of malignant cells in S phase. Examples of growth-inhibitory agents include agents that block cell cycle progression (at a place other than S phase), such as agents that induce G1 arrest and M-phase arrest. Classical M-phase blockers include the vincas (vincristine and vinblastine), taxol, and topo II inhibitors such as doxorubicin, daunorubicin, etoposide, and bleomycin. Those agents that arrest G1 also spill over into S-phase arrest, for example, DNA alkylating agents such as tamoxifen, prednisone, dacarbazine, mechlorethamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C. Further information can be found in The Molecular Basis of Cancer, Mendelsohn and Israel, eds., Chapter 1, entitled “Cell cycle regulation, oncogenes, and antineoplastic drugs” by Murakami et al. (WB Saunders: Philadelphia, 1995), especially p. 13. The 4D5 antibody (and functional equivalents thereof) can also be employed for this purpose if the cancer involves ErbB2-overexpressing cancer cells. See, e.g., WO 92/22653.

“Northern analysis” or “Northern blot” is a method used to identify RNA sequences that hybridize to a known probe such as an oligonucleotide, DNA fragment, cDNA or fragment thereof, or RNA fragment. The probe is labeled with a radioisotope such as ³²p, or by biotinylation, or with an enzyme. The RNA to be analyzed is usually electrophoretically separated on an agarose or polyacrylamide gel, transferred to nitrocellulose, nylon, or other suitable membrane, and hybridized with the probe, using standard techniques well known in the art such as those described in sections 7.39-7.52 of Sambrook et al., supra.

The technique of “polymerase chain reaction.” or “PCR.” as used herein generally refers to a procedure wherein minute amounts of a specific piece of nucleic acid, RNA and/or DNA, are amplified as described in U.S. Pat. No. 4,683,195 issued 28 Jul. 1987. Generally, sequence information from the ends of the region of interest or beyond needs to be available, such that oligonucleotide primers can be designed-, these primers, will be identical or similar in sequence to opposite strands of the template to be amplified. The 5′ terminal nucleotides of the two primers may coincide with the ends of the amplified material. PCR can be used to amplify specific RNA sequences, specific DNA sequences from total genomic DNA, and cDNA transcribed from total cellular RNA, bacteriophage, or plasmid sequences, etc. See generally Mullis et al., Cold Spring Harbor Symp. Quant. Biol., 51:263 (1987): Erlich. ed. PCR Technology. (Stockton Press, NY, 1989). As used herein, PCR is considered to be one, but not the only example of a nucleic acid polymerase reaction method for amplifying a nucleic acid test sample comprising the use of a known nucleic acid as a primer and a nucleic acid polymerase to amplify or generate a specific piece of nucleic acid.

II. Compositions and Methods of the Invention

A. Full-Length WISP Polypeptide

The present invention provides newly-identified and isolated nucleotide sequences encoding a polypeptide referred to in the present application as a WISP polypeptide, including a WISP-1, WISP-2, or WISP-3 polypeptide. In particular, cDNAs have been identified and isolated encoding novel murine and human WISP-1 and WISP-2, and human WISP-3 splice variants as disclosed in further detail in the Examples below.

Using BLAST and FastA sequence alignment computer programs, it was found that the coding sequences of mouse and human WISP-1 and -2, as well as the two coding sequences of human WISP-3 disclosed herein, show significant homology to DNA sequences disclosed in the GenBank database, including those published by Adams et al., Nature, 377:3-174 (1995).

Further, using BLAST and FastA sequence alignment computer programs, it was found that various portions of the coding sequences of mouse and human WISP-1 and WISP-2 show significant homology to CTGF, cef-10, Cyr61, and/or Nov protein. In this regard, mouse WISP-1 is 47% homologous to mouse CTGF and 46% homologous to human CTGF, mouse WISP-2 is 46% homologous to chick cef-10 protein precursor and 42% homologous to human Cyr61 protein, human WISP-1 is 47% homologous to mouse CTGF and 48% homologous to human CTGF, and human WISP-2 is 48% homologous to mouse CTGF, 49% homologous to human CTGF precursor, 46% homologous to mouse Nov protein homolog precursor, 49% homologous to human CTGF, and 48% homologous to mouse CTGF precursor. Further, apparently the amino acid sequences of mouse WISP-1 and mouse ELM 1 (Hashimoto et al., supra) are identical, and the amino acid sequences of human WISP-1 and mouse ELM1 are 84% identical.

Since these factors have also been correlated with IGFBPs, it is presently believed that the WISP-1 and WISP-2 polypeptides disclosed in the present application are newly identified members of the CTGF or IGFBP family and possess activity relating to development of normal, injured, and cancerous cells and tissue. More specifically, WISP-1 and WISP-2 may be involved in breast cancer, lung cancer, melanoma, and colon cancer, as well as in wound repair. Further, they may be involved in atherosclerosis.

Further, using BLAST and FastA sequence alignment computer programs, it was found that various portions of the coding sequences of the two splice variants of human WISP-3 show significant homology to mouse ELM1 and CTGF proteins. In this regard, both splice variants of WISP-3 are 45% homologous to mouse ELM1 and 42% homologous to mouse and human CTGF and its precursor, with the longer variant of FIG. 6 being 43% homologous to Xenopus CTGF and the shorter variant of FIG. 7 being 42% homologous to Xenopus CTGF.

B. WISP Polypeptide Variants

In addition to the full-length native-sequence WISP polypeptides described herein, it is contemplated that variants of these sequences can be prepared. WISP variants can be prepared by introducing appropriate nucleotide changes into the WISP-encoding DNA, or by synthesis of the desired variant WISP polypeptides. Those skilled in the art will appreciate that amino acid changes may alter posttranslational processes of the WISP polypeptide, such as changing the number or position of glycosylation sites or altering the membrane-anchoring characteristics, if the native WISP polypeptide is membrane bound.

Variations in the native full-length WISP sequences, or in various domains of the WISP polypeptides described herein, can be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S. Pat. No. 5,364,934. Variations may be a substitution, deletion, or insertion of one or more codons encoding the WISP polypeptide that results in a change in the amino acid sequence as compared with the native-sequence WISP polypeptide. Optionally the variation is by substitution of at least one amino acid with any other amino acid in any portion of the WISP polypeptide. Guidance in determining which amino acid residue may be inserted, substituted, or deleted without adversely affecting the desired activity may be found by comparing the sequence of the WISP polypeptide with that of homologous known CTGF protein molecules, in the case of WISP-1, WISP-2, and WISP-3, and minimizing the number of amino acid sequence changes made in regions of high homology. Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements. Insertions or deletions may optionally be in the range of 1 to about 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions, or substitutions of amino acids in the sequence and testing the resulting variants for activity in in vitro assays for gene upregulation or down regulation and in transgenic or knockout animals.

The variations can be made on the cloned DNA to produce the WISP DNA or WISP polypeptide variant DNA using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis (Carter et al., Nucl. Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)), cassette mutagenesis (Wells et al., Gene, 34:315-(1985)), alanine scanning, PCR mutagenesis, restriction selection mutagenesis (Wells et al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)), or other known techniques.

Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions. T. E. Creighton, Proteins: Structure and Molecular Properties (W.H. Freeman & Co., San Francisco, 1983); Chothia, J. Mol. Biol., 150:1 (1976). If alanine substitution does not yield adequate amounts of variant, an isoteric amino acid can be used.

Further deletional variants of the full-length WISP polypeptide include variants from which the N-terminal signal peptide, if any (such as, for example, those putatively identified as amino acids 1 to 22 for WISP-1, 1 to 23 for WISP2, 1-33 for the WISP-3 of FIG. 6 and 1-15 for the WISP-3 of FIG. 7), and/or the initiating methionine has been deleted.

C. Modifications of the WISP Polypeptide

Covalent modifications of the WISP polypeptides are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a WISP polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues. Derivatization with bifunctional agents is useful, for instance, for crosslinking a WISP polypeptide to a water-insoluble support matrix or surface for use in the method for purifying anti-WISP antibodies, and viceversa. Commonly used crosslinking agents include, e.g., 1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3′-dithiobis(succinimidylpropionate), bifunctional maleimides such as bis-N-maleimido-1,8-octane, and agents such as methyl-3-((p-azidophenyl)dithio)propioimidate.

Other modifications include deamidation of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues, respectively, hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the ∀-amino groups of lysine, arginine, and histidine side chains (Creighton, supra, pp. 79-86), acetylation of the N-terminal amine, and amidation of any C-terminal carboxyl group.

Another type of covalent modification of the WISP polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of the polypeptide. “Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in the native sequence (either by deleting the underlying glycosylation site or by removing the glycosylation moieties by chemical and/or enzymatic means) and/or adding one or more glycosylation sites that are not present in the native sequence. In addition, the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportion of the various sugar residues present.

Addition of glycosylation sites to the WISP polypeptide herein may be accomplished by altering the amino acid sequence. The alteration may be made, for example, by the addition of, or substitution by, one or more serine or threonine residues to the native sequence (for O-linked glycosylation sites). The amino acid sequence may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding the WISP polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids. The DNA mutation(s) may be made using methods described above.

Another means of increasing the number of carbohydrate moieties on the WISP polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, e.g., in WO 87/05330 published 11 Sep. 1987, and in Aplin and Wriston, CRC Crit. Rev. Biochem., pp. 259-306 (1981).

Removal of carbohydrate moieties present on the WISP polypeptide may be accomplished chemically or enzymatically or by mutational substitution of codons encoding amino acid residues that serve as targets for glycosylation. Chemical deglycosylation techniques are known in the art and described, for instance, by Hakimuddin, et al., Arch. Biochem. Biophys., 259:52 (1987) and by Edge et al., Anal. Biochem., 118:131 (1981). Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo- and exoglycosidases as described by Thotakura et al., Meth. Enzymol., 138:350 (1987).

Another type of covalent modification comprises linking the WISP polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes, in the manner set forth, e.g., in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.

The WISP polypeptide of the present invention may also be modified in a way to form a chimeric molecule comprising a WISP polypeptide, or a fragment thereof, fused to a heterologous polypeptide or amino acid sequence. In one embodiment, such a chimeric molecule comprises a fusion of the WISP polypeptide with a tag polypeptide which provides an epitope to which an anti-tag antibody can selectively bind. The epitope tag is generally placed at the amino- or carboxyl-terminus of a native or variant WISP molecule. The presence of such epitope-tagged forms can be detected using an antibody against the tag polypeptide. Also, provision of the epitope tag enables the WISP polypeptides to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag. In an alternative embodiment, the chimeric molecule may comprise a fusion of the WISP polypeptides, or fragments thereof, with an immunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule, such a fusion could be to the Fc region of an Ig, such as an IgG molecule.

Various tag polypeptides and their respective antibodies are well known in the art. Examples include poly-histidine (poly-His) or poly-histidine-glycine (poly-His-Gly) tags; the flu HA tag polypeptide and its antibody 12CA5 (Field et al., Mol. Cell. Biol., 8:2159-2165 (1988)); the c-myc tag and the 8F9, 3C7, 6E10r G4, B7, and 9E10 antibodies thereto (Evan et al., Molecular and Cellular Biology, 5:3610-3616 (1985)); and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody. Paborsky et al., Protein Engineering, 2 (6):547-553 (1990). Other tag polypeptides include the Flag-peptide (Hopp et al., BioTechnology, 6:1204-1210 (1988)); the KT3 epitope peptide (Martin et al., Science, 255:192-194 (1992)); an a-tubulin epitope peptide (Skinner et al., J. Biol. Chem., 266:15163-15166 (1991)); and the T7 gene 10 protein peptide tag. Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA, 87:6393-6397 (1990).

D. Preparation of WISP Polypeptide

The description below relates primarily to production of WISP polypeptides by culturing cells transformed or transfected with a vector containing at least DNA encoding the mature or full-length sequences of human or mouse WISP-1 (SEQ ID NOS:3, 4, 11, or 12, respectively), or containing at least DNA encoding the mature or full-length sequences of human or mouse WISP-2 (SEQ ID NOS:15, 16, 19, or 20, respectively), or containing at least DNA encoding the mature or full-length sequences of human WISP-3 of FIG. 6A-6C (SEQ ID NOS:32 or 33, respectively), or containing at least DNA encoding the mature or full-length sequences of human WISP-3 of FIG. 7A-7C (SEQ ID NOS:36 or 37, respectively).

It is, of course, contemplated that alternative methods, which are well known in the art, may be employed to prepare WISP polypeptides. For instance, the WISP polypeptide sequence, or portions thereof, may be produced by direct peptide synthesis using solid-phase techniques. See, e.g., Stewart et al., Solid-Phase Peptide Synthesis (W.H. Freeman Co.: San Francisco, Calif., 1969); Merrifield, J. Am. Chem. Soc., 85:2149-2154 (1963). In vitro protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be accomplished, for instance, using an Applied Biosystems peptide synthesizer (Foster City, Calif.) in accordance with manufacturer's instructions various portions of WISP polypeptides may be chemically synthesized separately and combined using chemical or enzymatic methods to produce a full-length WISP polypeptide.

1. Isolation of DNA Encoding WISP Polypeptide

DNA encoding a WISP polypeptide may be obtained from a cDNA library prepared from tissue believed to possess the mRNA for WISP polypeptide and to express it at a detectable level. Accordingly, DNA encoding human WISP polypeptide can be conveniently obtained from a cDNA library prepared from human tissue, such as a human fetal liver library or as otherwise described in the Examples. The gene encoding WISP polypeptide may also be obtained from a genomic library or by oligonucleotide synthesis.

A still alternative method of cloning WISP polypeptide is suppressive subtractive hybridization which is a method for generating differentially regulated or tissue-specific cDNA probes and libraries. This is described, for example, in Diatchenko et al. Proc. Natl. Acad. Sci. USA, 93:6025-6030 (1996). The procedure is based primarily on a technique called suppression, PCR and combines normalization and subtraction in a single procedure, The normalization step equalizes the abundance of cDNAs within the target population and the subtraction step excludes the common sequences between the target and driver populations.

Libraries can be screened with probes (such as antibodies to a WISP polypeptide or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the protein encoded by it. Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook et al., supra. An alternative means to isolate the gene encoding WISP polypeptide is to use PCR methodology. Sambrook et al., supra; Dieffenbach et al., PCR Primer: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1995).

The Examples below describe techniques for screening a cDNA library. The oligonucleotide sequences selected as probes should be of sufficient length and sufficiently unambiguous that false positives are minimized. The oligonucleotide is preferably labeled such that it can be detected upon hybridization to DNA in the library being screened. Methods of labeling are well known in the art, and include the use of radiolabels like 3-P-labeled ATP, biotinylation, or enzyme labeling. Hybridization conditions, including moderate stringency and high stringency, are provided in Sambrook et al., supra.

Sequences identified in such library screening methods can be compared and aligned to other known sequences deposited and available in public databases such as GenBank or other private sequence databases. Sequence identity (at either the amino acid or nucleotide level) within defined regions of the molecule or across the full-length sequence can be determined through sequence alignment using computer software programs such as ALIGN, DNAstar, and INHERIT which employ various algorithms to measure homology.

Nucleic acid having polypeptide-coding sequence may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequences disclosed herein for the first time, and, if necessary, using conventional primer extension procedures as described in Sambrook et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA.

2. Selection and Transformation of Host Cells

Host cells are transfected or transformed with expression or cloning vectors described herein for WISP polypeptide production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences. The culture conditions, such as media, temperature, pH, and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in Mammalian Cell Biotechnology: a Practical Approach, M. Butler, ed. (IRL Press, 1991) and Sambrook et al., supra.

Methods of transfection are known to the ordinarily skilled artisan, for example, CaPO-4 and electroporation. Depending on the host cell used, transformation is performed using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride, as described in Sambrook et al., supra, or electroporation is generally used for prokaryotes or other cells that contain substantial cell-wall barriers. Infection with Agrobacterium tumefaciens is used for transformation of certain plant cells, as described by Shaw et al., Gene, 23:315 (1983) and WO 89/05859 published 29 Jun. 1989. For mammalian cells without such cell walls, the calcium phosphate precipitation method of Graham and van der Eb, Virology, 52:456-457 (1978) can be employed. General aspects of mammalian cell host system trans format ions have been described in U.S. Pat. No. 4,399,216. Transformations into yeast are typically carried out according to the method of Van Solingen et al., J. Bact., 130:946 (19-77) and Hsiao et al., Proc. Natl. Acad. Sci. (USA), 76:3829 (1979) However, other methods for introducing DNA into cells, such as by nuclear microinjection, electroporation, bacterial protoplast fusion with intact cells, or polycations, e.g., polybrene or polyornithine, may also be used. For various techniques for transforming mammalian cells, see Keown et al., Methods in Enzymology, 185:527-537 (1990) and Mansour et al., Nature, 336:348-352 (1988).

Suitable host cells for cloning or expressing the DNA in the vectors herein include prokaryote, yeast, or higher eukaryote cells. Suitable prokaryotes include but are not limited to eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g., Salmonella typhimurium, Serratia, e.g., Serratia marcescans, and Shigella, as well as Bacilli such as B. subtilis and B. licheniformis (e.g., B. licheniformis 41P disclosed in DD 266,710 published 12 Apr. 1989). Pseudomonas such as P. aeruginosa, and Streptomyces. Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 31,446); E. coli X1776 (ATCC 31,537); E. coli strain W3110 (ATCC 27,325); and K5772 (ATCC 53,635). These examples are illustrative rather than limiting. Strain W3110 is one particularly preferred host or parent host because it is a common host strain for recombinant DNA product fermentations. Preferably, the host cell secretes minimal amounts of proteolytic enzymes. For example, strain W311G may be modified to effect a genetic mutation in the genes encoding proteins endogamous to the host, with examples of such hosts including E. coli W3110 strain 1A2, which has the complete genotype tonA; E. coli W3110 strain 9E4, which has the complete genotype tonA ptr3; E. coli W3110 strain 27C7 (AT-CC 55,244), which has the complete genotype tonA ptr3 phoA E15 (argF-lac)169 degP ompT kan^(r) ; E. coli W3110 strain 37D6, which has the complete genotype tonA ptr3 phoA E15 (argF-lac)169 degP ompT rbs7 ilvG kan^(r) ; E. coli W3110 strain 40B4, which is strain 37D6 with a non-kanamycin resistant degP deletion mutation; and an E. coli strain having mutant periplasmic protease disclosed in U.S. Pat. No. 4,946,783 issued 7 Aug. 1990. Alternatively, in vitro methods of cloning, e.g., PCR or other nucleic acid polymerase reactions, are suitable.

In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for vectors containing nucleic acid encoding WISP polypeptide. Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism. However, a number of other genera, species, and strains are commonly available and useful herein, such as Schizosaccharomyces pombe (Beach and Nurse, Nature, 290:140 (1981); EP 139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Pat. No. 4,943,529; Fleer et al., Bio/Technology, 9:968-975 (1991)) such as, e.g., K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et al., J. Bacteriol., 737 (1983)), K. fragilis (ATCC 12,424), K. bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii (ATCC 56,500), K. drosophilarum (ATCC 36,906; Van den Berg et al., Bio/Technology, 8:135 (1990)), K. thermotolerans, and K. marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070; Sreekrishna et al., J. Basic Microbiol., 28:265-278 (1988) Candida; Trichoderma reesia (EP 244, 234); Neurospora crassa (Case et al., Proc. Natl. Acad. Sci. USA, 76:5259-5263 (1979)); Schwanniomyces such as Schwanniomyces occidentalis (EP 394, 538 published 31 Oct. 1990); and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium (WO 91/00357 published 10 Jan. 1991), and Aspergillus hosts such as A. nidulans (Ballance et al., Biochem. Biophys. Res. Commun., 112:284-289 (1983); Tilburn et al., Gene, 26:205-221 (1983); Yelton et al., Proc. Natl. Acad. Sci. USA, 81:1470-1474 (1984)) and A. niger Kelly and Hynes, EMBO J., 4:475-479 (1985). Methylotropic yeasts are suitable herein and include, but are not limited to, yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula. A list of specific species that are exemplary of this class of yeasts may be found in C. Anthony, The Biochemistry of Methylotrophs, 269 (1982).

Suitable host cells for the expression of glycosylated WISP are derived from multicellular organisms. Examples of invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells. Examples of useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture (Graham et al., J. Gen Virol. 36:59 (1977)); Chinese hamster ovary cells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci. USA, 77:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod., 23:243-251 (1980); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); and mouse mammary tumor (MMT 060562, ATCC CCL51). The selection of the appropriate host cell is deemed to be within the skill in the art.

3. Selection and Use of a Replicable Vector

The nucleic acid (e.g., cDNA or genomic DNA) encoding the desired WISP polypeptide may be inserted into a replicable vector for cloning (amplification of the DNA) or for expression. Various vectors are publicly available. The vector may, for example, be in the form of a plasmid, cosmid, viral particle, or phage. The appropriate nucleic acid sequence may be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art. Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques which are known to the skilled artisan.

The desired WISP polypeptide may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which may be a signal sequence, if the WISP polypeptide is conducive to being secreted, or other polypeptide having a specific cleavage site at the N-terminus of the mature or full-length protein or polypeptide. In general, the signal sequence may be a component of the vector, or it may be a part of the DNA encoding the WISP polypeptide that is inserted into the vector. The signal sequence may be a prokaryotic signal sequence such as, for example, the alkaline phosphatase, penicillinase, lpp, or heat-stable enterotoxin II leaders. For yeast secretion the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader (including Saccharomyces and Kluyveromyces a-factor leaders, the latter described in U.S. Pat. No. 5,010,182), or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362,179 published 4 Apr. 1990), or the signal described in WO 90/13646 published 15 Nov. 1990. In mammalian cell expression, mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species, as well as viral secretory leaders, and including signals from WISP polypeptides.

Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2u plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV, or BPV) are useful for cloning vectors in mammalian cells.

Expression and cloning vectors will typically contain a selection gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.

An example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the nucleic acid encoding WISP polypeptide, such as DHFR or thymidine kinase. An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216 (1980). A suitable selection gene for use in yeast is the trp1 gene present in the yeast plasmid YRp7. Stinchcomb et al., Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979); Tschemper et al., Gene, 10:157 (1980). The trp1 gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1. Jones, Genetics, 85:12 (1977).

Expression and cloning vectors usually contain a promoter operably linked to the nucleic acid sequence encoding WISP polypeptide to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the B-lactamase and lactose promoter systems (Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature, 281:544 (1979)), alkaline phosphatase, a tryptophan (trp) promoter system (Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776), and hybrid promoters such as the tac promoter. deBoer et al., Proc. Natl. Acad. Sci. USA, 80:21-25 (1983). Promoters for use in bacterial systems also will contain a Shine-Dalgamo (S.D.) sequence operably linked to the DNA encoding the WISP polypeptide.

Examples of suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase (Hitzeman et al., J. Biol. Chem., 255:2073 (1980)) or other glycolytic enzymes (Hess et al., J. Adv. Enzyme Rea., 7:149 (1968); Holland, Biochemistry, 17:4900 (1978)), such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase.

Other yeast promoters, which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657.

WISP transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published 5 Jul. 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus, and Simian Virus 40 (SV40); from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter; and from heat-shock promoters, provided such promoters are compatible with the host cell systems.

Transcription of a DNA encoding a WISP polypeptide by higher eukaryotes may be increased by inserting an enhancer'sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription. Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, α-fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma,enhancer on the late side of the replication origin, and adenovirus enhancers. The enhancer may be spliced into the vector at a position 5′ or 3′ to the sequence coding for a WISP polypeptide, but is preferably located at a site 5′ from the promoter.

Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human, or nucleated cells from other multicellular organisms) will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5′ and, occasionally 3′, untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding WISP polypeptide.

Still other methods, vectors, and host cells suitable for adaptation to the synthesis of WISP polypeptides in recombinant vertebrate cell culture are described in Gething et al., Nature, 293:620-625 (1981); Mantei et al., Nature, 281:40-46 (1979); EP 117,060; and EP 117,058.

4. Detecting Gene Amplification/Expression

Gene amplification and/or expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA (Thomas, Proc. Natl. Acad. Sci. USA, 77:5201-5205 (1980)), dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.

Gene expression, alternatively, may be measured by immunological methods, such as immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product. Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native-sequence WISP polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence fused to DNA encoding WISP polypeptide and encoding a specific antibody epitope.

5. Purification of Polypeptide

Forms of WISP polypeptide may be recovered from culture medium or from host cell lysates. If membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g., Triton-X 100) or by enzymatic cleavage. Cells employed in expression of WISP polypeptides can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or cell lysing agents.

It may be desired to purify WISP polypeptide from recombinant cell proteins or polypeptides. The following procedures are exemplary of suitable purification procedures: by fractionation on an ion-exchange column; ethanol precipitation; reverse phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration using, for example, SEPHADEX™ G-75; protein A SEPHAROSE™ columns to remove contaminants such as IgG; and metal chelating columns to bind epitope-tagged forms of the WISP polypeptide. Various methods of protein purification may be employed, and such methods are known in the art and described, for example, in Deutscher, Methods in Enzymology, 182 (1990); and Scopes, Protein Purification: Principles and Practice (Springer-Veriag: New York, 1982).

In one specific example of purification, either a poly-His tag or the Fc portion of human IgG is added to the C-terminal coding region of the cDNA for WISP-1, WISP-2, or WISP-3 before expression. The conditioned media from the transfected cells are harvested by centrifrigation to remove the cells and filtered. For the poly-His-tagged constructs, the protein may be purified using a Ni-NTA column. After loading, the column may be washed with additional equilibration buffer and the protein eluted with equilibration buffer containing 0.25 M imidazole. The highly purified protein may then be desalted into a storage buffer if desired.

Immunoadhesin (Fc-containing) constructs of the WISP-1, WISP-2, and WISP-3 proteins may be purified from the conditioned media by pumping them onto a 5-ml Protein A column which had been equilibrated in a phosphate buffer. After loading, the column may be washed extensively with equilibration buffer before elution with citric acid. The eluted protein may be immediately neutralized by collecting 1-ml fractions into tubes containing TRIS buffer. The highly purified protein may be subsequently desalted into storage buffer as described above for the poly-His-tagged proteins. The homogeneity of the protein may be assessed by SDS polyacrylamide gels and by N-terminal amino acid sequencing by Edman degradation.

The purification step(s) selected will depend, for example, on the nature of the production process used and the particular WISP polypeptide produced.

E. Uses for WISP Polypeptide and its Nucleic Acid

Nucleotide sequences (or their complement) encoding WISP polypeptides have various applications in the art of molecular biology, including uses as hybridization probes, in chromosome and gene mapping, and in the generation of anti-sense RNA and DNA. Nucleic acid encoding WISP polypeptide will also be useful for the preparation of WISP polypeptides by the recombinant techniques described herein.

The full-length nucleotide sequences for mouse or human WTSP-1 or WISP-2 (SEQ ID NOS: 9, 1, 17, and 13, respectively), or portions thereof, or the full-length nucleotide sequences for human WISP-3 of FIG. 6 (SEQ ID NO:30) or for WISP-3 of FIG. 7 (SEQ ID NO:34) may be used as hybridization probes for a cDNA library to isolate or detect the full-length gene encoding the WISP polypeptide of interest or to isolate or detect still other genes (for instance, those encoding naturally occurring variants of WISP polypeptide, other WISP polypeptide family members, or WISP polypeptides from other species) which have a desired sequence identity to the WISP polypeptide sequences disclosed in FIGS. 1, 2, 3A and 3B, 4, 6A and 6B, and 7A and 7B (SEQ ID NOS: 3, 4, 11, 12, 15, 16, 19, 20, 32, 33, 36, or 37). For example, such procedures as in situ hybridization, Northern and Southern blotting, and PCR analysis may be used to determine whether DNA and/or RNA encoding a different WISP is present in the cell type(s) being evaluated. Optionally, the length of the probes will be about 20 to about 50 bases. For example, the hybridization probes may be derived from the UNQ228 (DNA33473-seq min) nucleotide sequence (SEQ ID NO:38) or the full-length human WISP-2 nucleotide sequence (SEQ ID NO:13) as shown in FIG. 4 or from genomic sequences including promoters, enhancer elements, and introns of DNA encoding native-sequence WISP polypeptide.

By way of example, a screening method will comprise isolating the coding region of the WISP gene using the known DNA sequence to synthesize a selected probe of about 40 bases. Hybridization probes may be labeled by a variety of labels, including radionucleotides such as ³²P or ³⁵S, or enzymatic labels such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems. Labeled probes having a sequence complementary to that of any of the genes encoding WISP polypeptides of the present invention can be used to screen libraries of human cDNA, genomic DNA, or mRNA to determine to which members of such libraries the probe hybridizes. Hybridization techniques are described in further detail in the Examples below.

The probes may also be employed in PCR techniques to generate a pool of sequences for identification of closely related WISP sequences.

Nucleotide sequences encoding a WISP polypeptide can also be used to construct hybridization probes for mapping the gene which encodes that WISP polypeptide and for the genetic analysis of individuals with genetic disorders. The nucleotide sequences provided herein may be mapped to a chromosome and specific regions of a chromosome using known techniques, such as in situ hybridization, linkage analysis against known chromosomal markers, and hybridization screening with libraries. If the amplification of a given gene is functionally relevant, then that gene should be amplified more than neighboring genomic regions which are not important for tumor survival. To test this, the gene can be mapped to a particular chromosome, e.g. by radiation-hybrid analysis. The amplification level is then determined at the location identified, and at neighboring genomic region. Selective or preferential amplification at the genomic region to which to gene has been mapped is consistent with the possibility that the gene amplification observed promotes tumor growth or survival. Chromosome mapping includes both framework and epicenter mapping. For further details see e.g., Stewart et al., Genome Research 7, 422-433 (1997)

Nucleic acid encoding a WISP polypeptide may be used as a diagnostic to determine the extent and rate of the expression of the DNA encoding the WISP polypeptide in the cells of a patient. To accomplish such an assay, a sample of a patient's cells is treated, via in situ hybridization, or by other suitable means, and analyzed to determine whether the sample contains mRNA molecules capable of hybridizing with the nucleic acid molecule.

Nucleic acids which encode WISP polypeptides or any of their modified forms can also be used to generate either transgenic animals or “knock-out” animals which, in turn, are useful in the development and screening of therapeutically useful reagents. A transgenic animal (e.g., a mouse or rat) is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage. A transgene is a DNA which is integrated into the genome of a cell from which a transgenic animal develops. In one embodiment, cDNA encoding a WISP polypeptide can be used to clone genomic DNA encoding the WISP polypeptide in accordance with established techniques and the genomic sequences used to generate transgenic animals that contain cells which express DNA encoding the WISP polypeptide.

Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Pat. Nos. 4,736,866 and 4,870,009 and WO 97/38086. Typically, particular cells would be targeted for WISP transgene incorporation with tissue-specific enhancers. Transgenic animals that include a copy of a transgene encoding the WISP polypeptide introduced into the germ line of the animal at an embryonic stage can be used to examine the effect of increased expression of DNA encoding the WISP polypeptide. Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression. In accordance with this facet of the invention, an animal is treated with the Teagent and a reduced incidence of the pathological condition, compared to untreated animals bearing the transgene, would indicate a potential therapeutic intervention for the pathological condition.

Alternatively, non-human homologues of WISP polypeptides can be used to construct a WISP polypeptide “knock-out” animal which has a defective or altered gene encoding a WISP polypeptide as a result of homologous recombination between the endogenous gene encoding the WISP polypeptide and altered genomic DNA encoding the WISP polypeptide introduced into an embryonic cell of the animal. For example, cDNA encoding the WISP polypeptide can be used to clone genomic DNA encoding the WISP polypeptide in accordance with established techniques. A portion of the genomic DNA encoding the WISP polypeptide can be deleted or replaced with another gene, such as a gene encoding a selectable marker which can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5′ and 3′ ends) are included in the vector. See e.g., Thomas and Capecchi, Cell, 51:503 (1987) for a description of homologous recombination vectors. The vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected. See e.g., Li et al., Cell, 69:915 (1992). The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras. See e.g., Bradley, in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152. A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term to create a “knock-out” animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knockout animals can be characterized, for instance, by their ability to defend against certain pathological conditions and by their development of pathological conditions due to absence of the WISP polypeptide.

In particular, assays in which CTGF, IGFBPs, and other members of the CTGF superfamily and other growth factors are usually used are preferably performed with the WISP-1 and WISP-2 polypeptides. For example, an assay to determine whether TGF-β induces the WISP polypeptide, indicating a role in cancer, may be performed as known in the art, as well as assays involving induction of cell death and ³H-thymidine proliferation assays. Mitogenic and tissue growth assays are also performed with the WISP polypeptide as set forth above. The results are applied accordingly.

The WISP polypeptides of the present invention may also be used to induce the formation of anti-WISP polypeptide antibodies, which are identified by routine screening as detailed below.

In addition to their uses above the WISP-1, WISP-2, and WISP-3 polypeptides of the present invention are useful as the basis for assays of IGF activity. Importantly, since such an as say measures a physiologically significant binding event, i.e., that of an IGF to its IGFBP, triggering a detectable change (such as phosphorylation, cleavage, chemical modification, etc.) It is unlikely to be both more sensitive and more accurate than immunoassays which detect the physiologically non-significant binding of an IGF to anti-WISP polypeptide antibody. Although more sensitive and accurate than antibodies, the WISP-1, WISP-2, and WISP-3 molecules of the invention can be used to assay IGF (such as IGF-I or IGF-II) levels in a sample in the same ways in which antibodies are used.

For diagnostic purposes, the WISP-1, WISP-2, or WISP-3 polypeptide can be used in accordance with immunoassay technology. Examples of immunoassays are provided by Wide at pages 199-206 of Radioimmune Assay Method, Kirkham and Huner. ed. E & S. Livingstone. Edinburgh. 1970.

Thus, in one embodiment. WISP-1, WISP-2, and WISP-3 polypeptides can be detectably labeled and incubated with a test sample containing IGF molecules (such as biological fluids, e.g., serum, sputum, urine, etc. ), and the amount of WISP-1, WISP-2, or WISP-3 molecule bound to the sample ascertained.

Immobilization of reagents is required for certain assay methods. Immobilization entails separating the WISP-1, WISP-2, or WISP-3 polypeptide from any analyte that remains free in solution. This conventionally is accomplished by either insolubilizing the WISP-1, WISP-2, or WISP-3 polypeptide before the assay procedure, as by adsorption to a water insoluble matrix or surface (Bennich et al. U.S. Pat. No. 3,720,760), by covalent coupling (for example, using glutaraldehyde cross-linking), or by insolubilizing the molecule afterward, e.g. by immunoprecipitation.

The foregoing are merely exemplary diagnostic assays for IGF. Other methods now or hereafter developed for the determination of these analytes are included within the scope hereof.

WISP-1, WISP-2, and WISP-3 polypeptides are also useful in radioimmunoassays to measure IGFs such as IGF-I or IGF-II. Such a radioimmunoassay would be conducted as described in the literature using the naturally purified or recombinant WISP-1, WISP-2 or WISP-3 as the WISP element.

In addition, WISP polypeptides are useful for screening for compounds that bind to them as defined above. Preferably, these compounds are small molecules such as organic or peptide molecules that exhibit one or more of the desired activities. Screening assays of this kind are conventional in the art, and any such screening procedure may be employed, whereby the test sample is contacted with the WISP polypeptide herein and the extent of binding and biological activity of the bound molecule are determined.

More specifically, this invention encompasses methods of screening compounds to identify those that mimic the WISP polypeptide (agonists) or prevent the effect of the WISP polypeptide (antagonists). Screening assays for antagonist drug candidates are designed to identify compounds that bind or complex with the WISP polypeptides encoded by the genes identified herein, or otherwise interfere with the interaction of the encoded polypeptides with other cellular proteins. Such screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates.

The assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays, and cell-based assays, which are well characterized in the art.

All assays for antagonists are common in that they call for contacting the drug candidate with a WISP polypeptide encoded by a nucleic acid identified herein under conditions and for a time sufficient to allow these two components to interact.

In binding assays, the interaction is binding and the complex formed can be isolated or detected in the reaction mixture. In a particular embodiment, the WISP polypeptide encoded by the gene identified herein or the drug candidate is immobilized on a solid phase, e.g., on a microtiter plate, by covalent or non-covalent attachments. Non-covalent attachment generally is accomplished by coating the solid surface with a solution of the WISP polypeptide and drying. Alternatively, an immobilized antibody, e.g., a monoclonal antibody, specific for the WISP polypeptide to be immobilized can be used to anchor it to a solid surface. The assay is performed by adding the non-immobilized component, which may be labeled by a detectable label, to the immobilized component, e.g., the coated surface containing the anchored component. When the reaction is complete, the non-reacted components are removed, e.g., by washing, and complexes anchored on the solid surface are detected. When the originally non-immobilized component carries a detectable label, the detection of label immobilized on the surface indicates that complexing occurred. Where the originally non-immobilized component does not carry a label, complexing can be detected, for example, by using a labeled antibody specifically binding the immobilized complex.

If the candidate compound interacts with but does not bind to a particular WISP polypeptide encoded by a gene identified herein, its interaction with that polypeptide can be assayed by methods well known for detecting protein-protein interactions. Such assays include traditional approaches, such as, e.g., cross-linking co-immunoprecipitation, and co-purification through gradients or chromatographic columns. In addition, protein-protein interactions can be monitored by using a yeast-based genetic system described by Fields and co-workers (Fields and Song, Nature (London), 340: 245-246 (1989); Chien et al., Proc. Natl. Acad. Sci. USA, 88: 9578-9582 (1991)) as disclosed by Chevray and Nathans, Proc. Natl. Acad. Sci. USA, 89: 5789-5793 (1991). Many transcriptional activators, such as yeast GAL4, consist of two physically discrete modular domains, one acting as the DNA-binding domain, the other one functioning as the transcription-activation domain. The yeast expression system described in the foregoing publications (generally referred to as the “two-hybrid system”) takes advantage of this property, and employs two hybrid proteins, one in which the target protein is fused to the DNA-binding domain of GAL4, and another, in which candidate activating proteins are fused to the activation domain. The expression of a GAL1-lacZ reporter gene under control of a GAL4-activated promoter depends on reconstitution of GAL4 activity via protein-protein interaction. Colonies containing interacting polypeptides are detected with a chromogenic substrate for β-galactosidase. A complete kit (MATCHMAKER™) for identifying protein-protein interactions between two specific proteins using the two-hybrid technique is commercially available from Clontech. This system can also be extended to map protein domains involved in specific protein interactions as well as to pinpoint amino acid residues that are crucial for these interactions.

Compounds that interfere with the interaction of a gene encoding a WISP polypeptide identified herein and other intra- or extracellular components can be tested as follows: usually a reaction mixture is prepared containing the product of the gene and the intra- or extracellular component under conditions and for a time allowing for the interaction and binding of the two products. To test the ability of a candidate compound to inhibit binding, the reaction is run in the absence and in the presence of the test compound. In addition, a placebo may be added to a third reaction mixture, to serve as positive control. The binding (complex formation) between the test compound and the intra- or extracellular component present in the mixture is monitored as described hereinabove. The formation of a complex in the control reaction(s) but not in the reaction mixture containing the test compound indicates that the test compound interferes with the interaction of the test compound and its reaction partner.

If the WISP polypeptide has the ability to stimulate the proliferation of endothelial cells in the presence of the co-mitogen ConA, then one example of a screening method takes advantage of this ability. Specifically, in the proliferation assay, human umbilical vein endothelial cells are obtained and cultured in 96-well flat-bottomed culture plates (Costar, Cambridge, Mass.) and supplemented with a reaction mixture appropriate for facilitating proliferation of the cells, the mixture containing Con-A (Calbiochem, La Jolla, Calif.). Con-A and the compound to be screened are added and after incubation at 37° C., cultures are pulsed with ³−H-thymidine and harvested onto glass fiber filters (phD; Cambridge Technology, Watertown, Mass.). Mean ³−(H)-thymidine incorporation (cpm) of triplicate cultures is determined using a liquid scintillation counter (Beckman Instruments, Irvine, Calif.). Significant ³−(H)thymidine incorporation indicates stimulation of endothelial cell proliferation.

To assay for antagonists, the assay described above is performed; however, in this assay the WISP polypeptide is added along with the compound to be screened and the ability of the compound to inhibit ³−(H)-thymidine incorporation in the presence of the WISP polypeptide indicates that the compound is an antagonist to the WISP polypeptide. Alternatively, antagonists may be detected by combining the WISP polypeptide and a potential antagonist with membrane-bound WISP polypeptide receptors or recombinant receptors under appropriate conditions for a competitive inhibition assay. The WISP polypeptide can be labeled, such as by radioactivity, such that the number of WISP polypeptide molecules bound to the receptor can be used to determine the effectiveness of the potential antagonist. The gene encoding the receptor can be identified by numerous methods known to those of skill in the art, for example, ligand panning and FACS sorting. Coligan et al., Current Protocols in Immun., 1 (2): Chapter 5 (1991). Preferably, expression cloning is employed wherein polyadenylated RNA is prepared from a cell responsive to the WISP polypeptide and a cDNA library created from this RNA is divided into pools and used to transfect COS cells or other cells that are not responsive to the WISP polypeptide. Transfected cells that are grown on glass slides are exposed to labeled WISP polypeptide. The WISP polypeptide can be labeled by a variety of means including iodination or inclusion of a recognition site for a site-specific protein kinase. Following fixation and incubation, the slides are subjected to autoradiographic analysis. Positive pools are identified and sub-pools are prepared and re-transfected using an interactive sub-pooling and re-screening process, eventually yielding a single clone that encodes the putative receptor.

As an alternative approach for receptor identification, labeled WISP polypeptide can be photo affinity-linked with cell membrane or extract preparations that express the receptor molecule. Cross-linked material is resolved by PAGE and exposed to X-ray film. The labeled complex containing the receptor can be excised, resolved into peptide fragments, and subjected to protein micro-sequencing. The amino acid sequence obtained from micro-sequencing would be used to design a set of degenerate oligonucleotide probes to screen a cDNA library to identify the gene encoding the putative receptor.

In another assay for antagonists, mammalian cells or a membrane preparation expressing the receptor would be incubated with labeled WISP polypeptide in the presence of the candidate compound. The ability of the compound to enhance or block this interaction could then be measured.

The compositions useful in the treatment of WISP-related disorders include, without limitation, antibodies, small organic and inorganic molecules, peptides, phosphopeptides, antisense and ribozyme molecules, triple-helix molecules, etc-, that inhibit the expression and/or activity of the target gene product.

More specific examples of potential antagonists include an oligonucleotide that binds to the WISP polypeptide, (poly)peptide-immunoglobulin fusions, and, in particular, antibodies including, without limitation, poly- and monoclonal antibodies and antibody fragments, single-chain antibodies, anti-idiotypic antibodies, and chimeric or humanized versions of such antibodies or fragments, as well as human antibodies and antibody fragments. Alternatively, a potential antagonist may be a closely related protein, for example, a mutated form of the WISP polypeptide that recognizes the receptor but imparts no effect, thereby competitively inhibiting the action of the WISP polypeptide.

Another potential WISP polypeptide antagonist is an antisense RNA or DNA construct prepared using antisense technology, where, e.g., an antisense RNA or DNA molecule acts to block directly the translation of mRNA by hybridizing to targeted mRNA and preventing protein translation. Antisense technology can be used to control gene expression through triple-helix formation or antisense DNA or RNA, both of which methods are based on binding of a polynucleotide to D13A or RNA. For example, the 5′ coding portion of the polynucleotide sequence, which encodes the mature WISP polypeptides herein, is used to design an antisense RNA oligonucleotide of from about 10 to 40 base pairs in length. A DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription (triple helix—see Lee et al., Nucl. Acids Res., 6: 3073 (1979); Cooney et al., Science, 241: 456 (1988); Dervan et al., Science, 251: 1360 (1991)), thereby preventing transcription and the production of the WISP polypeptide. The antisense RNA oligonucleotide hybridizes to the mRNA in vivo and blocks translation of the mRNA molecule into the WISP polypeptide (anti-sense,—Okano, Neurochem., 56: 560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression (CRC Press: Boca Raton, Fla., 1988). The oligonucleotides described above can also be delivered to cells such that the antisense RNA or DNA may be expressed in vivo to inhibit production of the WISP polypeptide. When antisense DNA is used, oligodeoxyribonucleotides derived from the translation-initiation site, e.g., between about −10 and +10 positions of the target gene nucleotide sequence, are preferred.

Potential antagonists include small molecules that bind to the active site, the receptor binding site, or growth factor or other relevant binding site of the WISP polypeptide, thereby blocking the normal biological activity of the WISP polypeptide. Examples of small molecules include, but are not limited to, small peptides or peptide-like molecules, preferably soluble peptides, and synthetic non-peptidyl organic or inorganic compounds.

Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. Ribozymes act by sequence-specific hybridization to the complementary target RNA, followed by endonucleolytic cleavage. Specific ribozyme cleavage sites within a potential RNA target can be identified by known techniques. For further details see, e.g., Rossi, Current Biology, 4: 469-471 (1994), and PCT publication No. WO 97/33551 (published Sep. 18, 1997).

Nucleic acid molecules in triple-helix formation used to inhibit transcription should be single-stranded and composed of deoxynucleotides. The base composition of these oligonucleotides is designed such that it promotes triple-helix formation via Hoogsteen base-pairing rules, which generally require sizeable stretches of purines or pyrimidines on one strand of a duplex. For further details see, e.g., PCT publication No. WO 97/33551, supra.

These small molecules can be identified by any one or more of the screening assays discussed hereinabove and/or by any other screening techniques well known for those skilled in the art.

WISP-1, WISP-2, and WISP-3 polypeptides are additionally useful in affinity purification of an 1GF that binds to WISP-1, WISP-2, or WISP-3 (such as, for example, IGF-I) and in purifying antibodies thereto. The WISP-1, WISP-2, or WISP-3 is typically coupled to an immobilized resin such as Affi-Gel 10™ (Bio-Rad. Richmond, Calif.) or other such resins (support matrices) by means well known in the art. The resin is equilibrated in a buffer (such as one containing 150 mM NaCl, 20 mM HEPES, pH 7.4 supplemented to contain 20% glycerol and 0.5% NP-40) and the preparation to be purified is placed in contact with the resin, whereby the molecules are selectively adsorbed to the WISP-1, WISP-2, or WISP-3 on the resin.

The resin is then sequentially washed with suitable buffers to remove non-adsorbed material, including unwanted contaminants, from the mixture to be purified, using, e.g. 150 mM NaCl, 20 mM HEPES, pH 7.4, containing 0.5% NP-40: 150 mM NaCl, 20 mM HEPES, pH 7.4 containing 0.5 M NaCl and 0.1% NP-40: 150 mM NaCl, 20 mM HEPES, pH 7.4 containing 0.1% deoxycholate: 150 mM NaCl, 20 mM HEPES, pH 7.4 containing 0.1% NP-40: and a solution of 0.1% NP-40, 20% glycerol and 50 mM glycine, pH 3. The resin is then treated so as to elute the 1GF using a buffer that will break the bond between the 1GF and WISP-1, WISP-2, or WISP-3 (using, e.g. 50 mM glycine, pH 3, 0.1% NP-40, 20% glycerol, and 100 mM NaCl).

It is contemplated that the WISP polypeptides of the present invention may be used to treat various conditions, including those characterized by overexpression and/or activation of at least the Wnt pathway. Further, since the WISP-1, WISP-2, and WISP-3 molecules respond to hormone-expressed breast cancer in mice and are abnormally expressed in human cancer, and are over-amplified in various colon cancer cell lines, they are useful in diagnosing cancer, for example, as a marker for increased susceptibility to cancer or for having cancer. Exemplary conditions or disorders to be treated with the WISP polypeptides include benign or malignant tumors (e.g., renal, liver, kidney, bladder, testicular, breast, gastric, ovarian, colorectal, prostate, pancreatic, lung, esophageal, vulval, thyroid, hepatic carcinomas; sarcomas; glioblastomas; and various head and neck tumors); leukemias and lymphoid malignancies; other disorders such as neuronal, glial, astrocytal, hypothalamic, and other glandular, macrophagal, epithelial, stromal, and blastocoelic disorders; cardiac disorders; renal disorders; catabolic disorders; bone-related disorders such as osteoporosis; and inflammatory, angiogenic, and immunologic disorders, such as arteriosclerosis; as well as connective tissue disorders, including wound healing.

The WISP polypeptides of the invention are administered to a mammal, preferably a human, in accord with known methods, such as intravenous administration as a bolus or by continuous infusion over a period of time, by intramuscular, intraperitoneal, intracerebrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, oral, topical, or inhalation routes. Intravenous or subcutaneous administration of the polypeptide is preferred.

Therapeutic formulations of the WISP polypeptide are prepared for storage by mixing the polypeptide having the desired degree of purity with optional pharmaceutically acceptable carriers, excipients, or stabilizers (Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980)), in the form of lyophilized formulations or aqueous solutions. Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccha rides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose, or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™, or polyethylene glycol (PEG).

Other therapeutic regimens may be combined with the administration of the WISP polypeptides of the instant invention. For example, the patient to be treated with the polypeptides disclosed herein may also receive radiation therapy if the disorder is cancer. Alternatively, or in addition, a chemotherapeutic agent may be administered to the patient with cancer. Preparation and dosing schedules for such chemotherapeutic agents may be used according to manufacturers' instructions or as determined empirically by the skilled practitioner. Preparation and dosing schedules for such chemotherapy are also described in Chemotherapy Service, Ed., M. C. Perry (Williams & Wilkins: Baltimore, Md., 1992). The chemotherapeutic agent may precede or follow administration of the polypeptide or may be given simultaneously therewith. The polypeptide may be combined with an anti-oestrogeri compound such as tamoxifen or an anti-progesterone such as onapristone (see, EP 616812) in dosages known for such molecules.

It may be desirable also to co-administer with the WISP polypeptide (or anti-WISP polypeptide) antibodies against other tumor-associated antigens, such as antibodies which bind to HER-2, EGFR, ErbB2, ErbB3, ErbB4, or vascular endothelial factor (VEGF). Alternatively, or in addition, two or more different anti-cancer antibodies, such as anti-ErbB2 antibodies, may be co-administered to the patient with the WISP polypeptide (or anti-WISP polypeptide antibody). Sometimes, it may be beneficial also to administer one or more cytokines to the patient.

In a preferred embodiment, the WISP polypeptide is co-administered with a growth-inhibitory agent to the cancer patient. For example, the growth-inhibitory agent may be administered first, followed by the WISP polypeptide. However, simultaneous administration or administration of the WISP polypeptide first is also contemplated. Suitable dosages for the growth-inhibitory agent are those presently used and may be lowered due to the combined action (synergy) of the growth-inhibitory agent and polypeptide. The antibodies, cytotoxic agents, cytokines, or growth-inhibitory agents are suitably present in combination in amounts that are effective for the purpose intended.

The active ingredients may also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethyl cellulose or gelatin microcapsules and poly-(methylmethacylate)microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nanoparticles, and nanocapsules) or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences, 16th edition, Osol, A. Ed. (1980), supra.

The formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.

Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the polypeptide, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and y ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT™ (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(−)-3-hydroxybutyric acid. While polymers such as ethylene7vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods. When encapsulated polypeptides remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37° C., resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S—S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions.

For the prevention or treatment of disease or disorder, the appropriate dosage of WISP polypeptide will depend on the type of disorder to be treated, as defined above, the severity and course of the disorder, whether the polypeptide is administered for preventive or therapeutic purposes, previous therapy, the patient's clinical history and response to the polypeptide, the route of administrazion, the condition of the patient, and the discretion of the attending physician. The polypeptide is suitably administered to the patient at one time or over a series of treatments.

Depending on the type and severity of the disease, about 1 μg/kg to 15 mg/kg (e.g., 0.1-20 mg/kg) of WISP polypeptide is an initial candidate dosage for administration to the patient, whether, for example, by one or more separate administrations, or by continuous infusion. A typical daily dosage might range from about 1 μg/kg to 100 mg/kg or more, depending on the factors mentioned above. For repeated administrations over several days or longer, depending on the condition, the treatment is sustained until a desired suppression of symptoms of the disorder occurs. However, other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques and assays. In another embodiment of the invention, an article of manufacture containing materials useful for the treatment of the disorders described above is provided. The article of manufacture comprises a container and a label. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition which is effective for treating the condition and may have a sterile access port (for example, the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The active agent in the composition is the WISP polypeptide. The label on, or associated with, the container indicates that the composition is used for treating the condition or disorder of choice. The article of manufacture may further comprise a second container comprising a pharmaceutically acceptable buffer, such as phosphate-buffered saline, Ringer's solution, and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.

F. Anti-WISP Polypeptide Antibodies

The present invention further provides anti-WISP polypeptide antibodies. Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies.

1. Polyclonal Antibodies

The anti-WISP polypeptide antibodies of the present invention may comprise polyclonal antibodies. Methods of preparing polyclonal antibodies are known to the skilled artisan. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. The immunizing agent may include the WISP polypeptide or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Examples of adjuvants which may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation.

2. Monoclonal Antibodies

The anti-WISP polypeptide antibodies may, alternatively, be monoclonal antibodies. Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256: 4 95 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in vitro.

The immunizing agent will typically include the WISP polypeptide or a fusion protein thereof. Generally, either peripheral blood lymphocytes (“PBLs”) are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as PEG, to form a hybridoma cell. Goding, Monoclonal Antibodies: Principles and Practice (Academic Press: New York, 1986) pp. 59-103. Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine, and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (“HAT medium”), which substances prevent the growth of HGPRT-deficient cells.

Preferred immortalized cell lines are those that fuse efficiently, support stable high-level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, Calif., and the American Type Culture Collection, Manassas, Va. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies. Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications (Marcel Dekker, Inc.: New York, 1987) pp. 51-63.

The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against a WISP polypeptide. Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem., 107: 220 (1980).

After the desired hybridoma cells are identified, the clones may be subcloned by limiting dilution procedures and grown by standard methods. Goding, supra. Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells may be grown in vivo as ascites in a mammal.

The monoclonal antibodies secreted by the subclones may be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.

The monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA may be placed into expression vectors, which are then transfected into host cells such as simian COS cells, CHO cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also may be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences (U.S. Pat. No. 4,816,567; Morrison et al., Proc. Natl. Acad. Sci. USA, 81: 6851-6855 (1984)) or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.

The antibodies may be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain. The heavy chain is truncated generally at any point in the Fc region so as to prevent heavy-chain crosslinking. Alternatively, the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking.

In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly Fab fragments, can be accomplished using routine techniques known in the art.

3. Humanized Antibodies

The anti-WISP antibodies of the invention may further comprise humanized antibodies or human antibodies. Humanized forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains, or fragments thereof (such as Fv, Fab, Fab′, F(ab′)₂, or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary-determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat, or rabbit having the desired specificity, affinity, and capacity. In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin, and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody preferably also will comprise at least a portion of an Fc, typically that of a human immunoglobulin. Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988); Presta, Curr. Op. Struct. Biol., 2:593-596 (1992).

Methods for humanizing non-human antibodies are well known in the art. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain. Humanization can be essentially performed following the method of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such “humanized” antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.

Human antibodies can also be produce a using various techniques known in the art, including phage-display libraries. Hoogenboom and Winter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol., 222:581 (1991). The techniques of Cole et al. and Boemer et al. are also available for the preparation of human monoclonal antibodies. Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 7? (1985); Boemer et al., J. Immunol., 147(1):86-95 (1991).

4. Bispecific Antibodies

Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for a WISP polypeptide; the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit.

Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities. Milstein and Cuello, Nature, 305:537-539 (1983). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published 13 May 1993, and in Traunecker et al., EMBO J., 10: 3655-3659 (1991).

Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant-domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions, it is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al., Methods in Enzymology, 121-210 (1986).

5. Heteroconjugate Antibodies

Heteroconjugate antibodies are also within the scope of the present invention. Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Pat. No. 4,676,980), and for treatment of HIV infection. WO 91/00360; WO 92/200373; EP 03089. It is contemplated that the antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving cross-linking agents. For example, immunotoxins may be constructed using a disulfide-exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Pat. No. 4,676,980.

G. Uses for Anti-WISP Polypeptide Antibodies

The antibodies of the invention may be used as affinity purification agents. In this process, the antibodies are immobilized on a solid phase such a SEPHADEX™ resin or filter paper, using methods well known in the art. The immobilized antibody is contacted with a sample containing the WISP polypeptide (or fragment thereof) to be purified, and thereafter the support is washed with a suitable solvent that will remove substantially all the material in the sample except the WISP protein, which is bound to the immobilized antibody. Finally, the support is washed with another suitable solvent, such as glycine buffer, pH 5.0, that will release the WISP polypeptide from the antibody.

Anti-WISP polypeptide antibodies may also be useful in diagnostic assays for WISP polypeptide, e.g., detecting its expression in specific cells, tissues, or serum. Thus, the antibodies may be used in the diagnosis of human malignancies (see, for example, U.S. Pat. No. 5,183,884).

For diagnostic applications, the antibody typically will be labeled with a detectable moiety. Numerous labels are available which can be preferably grouped into the following categories:

(a) Radioisotopes, such as ³⁵s, ¹⁴C, ¹²⁵I, ³H, and ¹³¹I. The antibody can be labeled with the radioisotope using the techniques described in Current Protocols in Immunology, Volumes 1 and 2. Coligen et al, Ed., (Wiley-Interscience: New York, 1991), for example, and radioactivity can be measured using scintillation counting.

(b) Fluorescent labels such as rare earth chelates (europium chelates) or fluorescein and its derivatives, rhodamine and its derivatives, dansyl, Lissamine, phycoerythrin, and Texas Red are available. The fluorescent labels can be conjugated to the antibody using the techniques disclosed in Current Protocols in Immunology, supra, Coligen, ed., for example. Fluorescence can be quantified using a fluorimeter.

(c) Various enzyme-substrate labels are available, and U.S. Pat. No. 4,275,149 provides a review of some of these. The enzyme preferably catalyzes a chemical alteration of the chromogenic substrate which can be measured using various techniques. For example, the enzyme may catalyze a color change in a substrate, which can be measured spectrophotometrically. Alternatively, the enzyme may alter the fluorescence or chemiluminescence of the substrate. Techniques for quantifying a change in fluorescence are described above. The chemiluminescent substrate becomes electronically excited by a chemical reaction and may then emit light which can be measured (using a chemiluminometer, for example) or donates energy to a fluorescent acceptor. Examples of enzymatic labels include luciferases (e.g., firefly luciferase and bacterial luciferase; U.S. Pat. No. 4,737,456), luciferin, 2,3-dihydrophthalazinediones, malate dehydrogenase, urease, peroxidase such as horseradish peroxidase (HRPO), alkaline phosphatase, β-galactosidase, glucoamylase, lysozyme, saccharide oxidases (e.g., glucose oxidase, galactose oxidase, and glucoge-6-phosphate dehydrogenase), heterocyclic oxidases (such as uricase and xanthine oxidase), lactoperoxidase, microperoxidase, and the like. Techniques for conjugating enzymes to antibodies are described in O'Sullivan et al., Methods for the Preparation of Enzyme-Antibody Conjugates for use in Enzyme Immunoassay, in Methods in Enzym., Vol. 73, Langone and Van Vunakis, eds. (New York: Academic Press, 1981), pp. 147-166.

Examples of enzyme-substrate combinations include:

(i) Horseradish peroxidase (HRPO) with hydrogen peroxidase as a substrate, wherein the hydrogen peroxidase oxidizes a dye precursor (e.g., orthophenylene diamine (OPD) or 3,3′,5,5′-tetramethyl benzidine hydrochloride (TMB));

(ii) alkaline phosphatase (AP) with para-nitrophenyl phosphate as chromogenic substrate; and

(iii) β-D-galactosidase (β-D-Gal) with a chromogenic substrate (e.g., p-nitrophenyl-β-D-galactosidase) or fluorogenic substrate (4-methylumbelliferyl-β-D-galactosidase).

Numerous other enzyme-substrate combinations are available to those skilled in the art. For a general review of these, see, for example, U.S. Pat. Nos. 4,275,149 and 4,318,980.

Sometimes, the label is indirectly conjugated with the antibody. The skilled artisan will be aware of various techniques for achieving this. For example, the antibody can be conjugated with biotin and any of the three broad categories of labels mentioned above can be conjugated with avidin, or vice versa. Biotin binds selectively to avidin, and thus, the label can be conjugated with the antibody in this indirect manner. Alternatively, to achieve indirect conjugation of the label with the antibody, the antibody is conjugated with a small hapten (e.g., digoxin) and one of the different types of labels mentioned above is conjugated with an anti-hapten antibody (e.g., anti-digoxin antibody). Thus, indirect conjugation of the label with the antibody can be achieved.

In another embodiment of the invention, the anti-WISP polypeptide antibody need not be labeled, and the presence thereof can be detected using a labeled antibody which binds to the anti-WISP polypeptide antibody.

The antibodies of the present invention may be employed in any known assay method, such as competitive binding assays, direct and indirect sandwich assays, and immunoprecipitation assays. Zola, Monoclonal Antibodies: A Manual of Techniques (New York: CRC Press, Inc., 1987), pp.147-158.

Competitive binding assays rely on the ability of a labeled standard to compete with the test sample analyte for binding with a limited amount of antibody. The amount of WISP protein in the test sample is inversely proportional to the amount of standard that becomes bound to the antibodies. To facilitate determining the amount of standard that becomes bound, the antibodies preferably are insolubilized before or after the competition, so that the standard and analyte that are bound to the antibodies may conveniently be separated from the standard and analyte which remain unbound.

Sandwich assays involve the use of two antibodies, each capable of bincting to a different immunogenic portion, or epitope, of the protein to be detected. In a sandwich assay, the test sample analyte is bound by a first antibody which is immobilized on a solid support, and thereafter a second antibody binds to the analyte, thus forming an insoluble three-part complex. See, e.g., U.S. Pat No. 4,376,110. The second antibody may itself be labeled with a detectable moiety (direct sandwich assays) or may be measured using an anti-immunoglobulin antibody that is labeled with a detectable moiety (indirect sandwich assay). For example, one type of sandwich assay is an ELISA assay, in which case the detectable moiety is an enzyme.

For immunohistochemistry, the tumor sample may be fresh or frozen or may be embedded in paraffin and fixed with a preservative such as formalin, for example.

The antibodies may also be used for in vivo diagnostic assays. Preferably, the antibody is labeled with a radionuclide (such as ¹¹¹In, ⁹⁹Tc, ¹⁴C, ¹³¹I, ¹²⁵I, ³H, ³²P or ³⁵S) so that the tumor can be localized using immunoscintiography.

Additionally, anti-WISP polypeptide antibodies may be useful as antagonists to WISP polypeptide functions where WISP polypeptide is upregulated in cancer cells or stimulates their prolilferation or is upregulated in atheroscierotie-tissue. Hence, for example, the anti-WISP polypeptide antibodies may by themselves or with a chemotherapeutic agent or other cancer treatment or drug such as anti-HER-2 antibodies be effective in treating certain forms of cancer such as breast cancer, colon cancer, lung cancer, and melanoma. Further uses for the antibodies include inhibiting the binding of a WISP polypeptide to its receptor, if applicable, or to an IGF, if applicable. For therapeutic use, the antibodies can be used in the formulations, schedules, routes, and doses indicated above under uses for the WISP polypeptides. In addition, anti-WISP polypeptide antibody may be administered into the lymph as well as the blood stream.

As a matter of convenience, the anti-WISP antibody of the present invention can be provided as an article of manufacture such as a kit. An article of manufacture containing a WISP polypeptide or antagonists thereof useful for the diagnosis or treatment of the disorders described above comprises at least a container and a label. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition that is effective for diagnosing or treating the condition and may have a sterile access port (for example, the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).

The active agent in the composition is the WISP polypeptide or an agonist or antagonist thereto. The label on, or associated with, the container indicates that the composition is used for diagnosing or treating the condition of choice. The article of manufacture may further comprise a second container comprising a pharmaceutically-acceptable buffer, such as phosphate-buffered saline, Ringer's solution, and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use. The article of manufacture may also comprise a second or third container with another active agent as described above. A kit format generally is a packaged combination of reagents in predetermined amounts with instructions for performing the diagnostic or treatment assay.

If the active agent is an antibody that is labeled with an enzyme, the kit will include substrates and cofactors required by the enzyme (e.g., a substrate precursor which provides the detectable chromophore or fluorophore). In addition, other additives may be included such as stabilizers, buffers (e.g., a block buffer or lysis buffer), and the like. The relative amounts of the various reagents may be varied widely to provide for concentrations in solution of the reagents which substantially maximize the sensitivity of the assay. Particularly, the reagents may be provided as dry powders, usually lyophilized, including excipients which on dissolution will provide a reagent solution having the appropriate concentration.

The following examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way.

All patent and literature references cited in the present specification are hereby incorporated by reference in their entirety.

EXAMPLES

Commercially available reagents referred to in the examples were used according to manufacturer's instructions unless otherwise indicated. The source of those cells identified in the following examples, and throughout the specification, by ATCC accession numbers is the American Type Culture Collection, 10801 University Blvd., Manassas, Va.

Example 1 Isolation of cDNA Clones Encoding Mouse WISP-1

Several putative WISP genes have been identified at the mRNA level in a high-throughput PCR-select cDNA substraction experiment carried out using a mouse mammary cell line (C57MG), which has been transformed by a Wnt-1 retroviral vector and compared with the parental cell line. The WISP family disclosed herein, including the mouse WISP-1 gene, was induced only in the transformed cell line C57MGWnt-1.

1. Suppression Subtractive Hybridization

Mouse WISP-1 was isolated independently by Wnt-1 differential screening using suppression subtractive hybridization (SSH), as described by Diatchenko et al., Proc. Natl. Acad. Sci. USA, 93: 6025-6030 (1996). SSH was carried out using the PCR-SELECT®R cDNA Subtraction Kit (Clontech Laboratories, Inc.) according to the manufacturer's protocol. Driver double-stranded (ds) cDNA was synthesized from 2 micrograms of polyA+ RNA isolated from a mouse mammary cell line (C57MG), obtainable from a mouse breast cancer myoepithelial cell line. This cell line is described in Brown et al., Cell, 46: 1001-1009 (1986); Olson and Papkoff, Cell Growth and Differentiation, 5: 197-206 (1994); Wong et al., Mol. Cell. Biol., 14: 6278-6286 (1994); and Jue et al., Mol. Cell. Biol., 12: 321-328 (1992), and is responsive to Wnt-1 but not to Wnt-4. Tester ds cDNA was synthesized from 2 micrograms of polyA+ RNA isolated from a transformed version of C57MG, called C57MG/wnt-1.

The C57MG/wnt-1 mouse mammary derivative cell line was prepared by first transforming the parent line with a Wnt-1 retroviral vector, pBabe Puro (5.1 kb). This vector has a 5′ LTR, packaging elements, a multiple cloning site, the puromycin-resistance gene driven off the SV40 promoter, a 3′ LTR, and the bacterial elements for replication and ampicillin selection. The vector was modified slightly for Wnt-1 cloning by removing the HindIII site after the SV40 promoter and adding a HindIII site to the multiple cloning site. Wnt-1 is cloned from EcoRI-HindIII in the multiple cloning site. FIG. 13 shows a map of the vector.

The transformed derivative cells were grown up in a conventional fashion, and the final cell population was selected in DMEM+10% FCS with 2.5 μg/ml puromycin to stabilize the expression vector.

PCR was performed using the Clontech kit, including the cDNA synthesis primer (SEQ ID NO:40), adaptors 1 and 2 (SEQ ID NOS:41 and 42, respectively) and complementary sequences for the adaptors (SEQ ID NOS: 43 and 44, respectively), PCR primer 1 (SEQ ID NO:45), PCR primer 2 (SEQ ID NO:46), nested PCR primer 1 (SEQ ID NO:47), nested PCR primer 2 (SEQ ID NO:48), control primer G3PDH5′ primer (SEQ ID NO:49), and control primer G3PDH3′ primer (SEQ ID NO:50), shown in FIG. 14.

Products generated from the secondary PCR reaction were inserted into the cloning site region of pGEM-T vector (Promega), shown in FIG. 15 (SEQ ID NOS: 51 and 52 for 5′ and 3′ sequences, respectively). Plasmid DNAs were prepared using the WIZARD MINIPREP™ Kit (Promega). DNA sequencing of the subcloned PCR fragments was performed manually by the chain termination reaction (SEQUENASE 2.0™ Kit, Pharmacia). Nucleic acid homology searches were performed using the BLAST program noted above.

A total of 1384 clones were sequenced out of greater than 5000 tound. A total of 1996 DNA templates were prepared. A program was used to trim the vector off, and a different program used to cluster the clones into two or more identical clones or with an overlap of 50 bases the same., Then a BLAST was performed of a representative clone from the cluster. Primers were designed for RT-PCR to see if the clones were differentially expressed.

2. Semi-Quantitative RT-PCR

One of the clones was clone 568 having 71 bp, which was identified as encoding mouse WISP-1. There were six clones in this cluster. The nucleotide sequence and putative amino acid sequence of full-length mouse WISP-1 are shown in FIGS. 1A-1B (SEQ ID NOS: 9 and 12, respectively). RT-PCR primers were designed for confirming differential expression, screening for full-length mouse clone, and screening for the human clone. These primers were 568.PCR.top1 (nucleotides 909-932 of the full-length nucleotide sequence encoding mouse WISP-1 (SEQ ID NO:9) of FIGS. 1A-1B) and 568.PCR.bot1 (nucleotides 955-978 of the full-length complementary nucleotide sequence encoding mouse WISP-1 (SEQ ID NO:10) of FIGS. 1A-1B), which are as follows: (SEQ ID NO:100) 568.PCR.top1: 5′-CCAGCCAGAGGAGGCCACGAAC (SEQ ID NO:101) 568.PCR.bot1: 3′-TGTGCGTGGATGGCTGGGTTCATG

For the RT-PCR procedure, cell lines were grown to subconfluence before extracting the RNA. Total RNA was extracted using Stat-60™ (TEL-TEST™ B) per manufacturer's instructions. First-strand cDNA was prepared from 0.1 μg-3 μg of total RNA with the SUPERSCRIPT™ RT kit (Gibco, BRL). PCR amplification of 5 μl of first-strand cDNA was performed in a 50-μl PCR reaction. The above primers were used to amplify first-strand cDNA. As controls, primers corresponding to nucleotide positions 707-729 (sense; 5′-GTGGCCCATGCTCTGGCAGAGGG (SEQ ID NO:102)) or 836-859 (sense; 5′-GACTGGAGCAAGGTCGTCCTCGCC (SEQ ID NO:103)) and 1048-1071 (anti-sense; 5′-GCACCACCCACAAGGAAGCCATCC (SEQ ID NO:104)) of human triosephosphate isomerase (huTPI) (Maquat et al., J. Biol. Chem., 260: 3748-3753 (1985); Brown et al., Mol. Cell. Biol., 5: 1694-1706 (1985)) were used to amplify first-strand cDNA. For mouse triosephosphate isomerase, primers corresponding to nucleotide positions 433-456 (sense; 51-GACGAAAGGGAAGCCGGCATCACC (SEQ ID NO:105)) or 457-480 bp (sense; 51-GAGAAGGTCGTGTTCGAGCAAACC (SEQ ID NO:106)) and 577-600 bp (antisense; 51-CTTCTCGTGTACTTCCTGTGCCTG (SEQ ID NO:107)) or 694-717 bp (antisense; 5′-CACGTCAGCTGGCGTTGCCAGCTC (SEQ ID NO:108)) were used for amplification.

Briefly, 4 μCi of (³²P-)CTP (3000 Ci/mmol) was added to each reaction with 2.5 U of TAKARA EX TAQ™ (PanVera, Madison, Wis.) and 0.2 μM of each dNTP. The reactions were amplified in a 480 PCR THERMOCYCLER™ (Perkin Elmer) using the following conditions: 94° C. for 1 min., 62° C. for 30 sec., 72° C. for 1 min, for 18-25 cycles. 5 μl of PCR products were electrophoresed on a 6% polyacrylamide gel. The gel was exposed to film. Densitometry measurements were obtained using ALPHA EASE VERSION 3.3a™ software (Alpha Innotech Corporation) to quantitate the WISP-or TPI-specific gene products.

3. Northern Blot Analysis

Adult multiple-tissue Northern blots (Clontech) and the Northern blot of the C57MG parent and C57MG/Wnt-1 derivative polyA+RNA (2 μg/lane) were hybridized with a 70-bp mouse WISP-1 probe (amino acids 278 through 300 of FIG. 1A-1B; QPEEATNFTLAGCVSTRTYRPKY; SEQ ID NO:109) generated using the primers 568.PCR.top1 and 568.pcr.bot1 noted above. The membranes were washed in 0.1×SSC at 55-65° C. and exposed for autoradiography. Blots were rehybridized with a 75-bp synthetic probe from the human actin gene. See Godowski et al., Proc. Natl. Acad. Sci. USA, 86: 8083-8087 (1989) for a method for making a probe with overlapping oligos, which is how the actin probe was prepared.

4. cDNA Library Screening

Clones encoding the full-length mouse WISP-1 were isolated by screening a Xgt1O oligodT primed mouse embryo library (Clontech) with the primers 568.PCR.top1 and 568.PCR.bot1 noted above. The inserts of 13 of these clones were subcloned into PBLUESCRIPT™ IISK+ and their DNA sequences determined by dideoxy DNA sequencing on both strands.

5. Results

The recently described technique of SSH combines a high subtraction efficiency with an equalized representation of differentially expressed sequences. This method is based on specific PCR reactions that permit exponential amplification of cDNAs which differ in abundance, whereas amplification of sequences of identical abundance in two populations is suppressed. The SSH technique was used herein to isolate genes expressed in a mouse mammary myoepithelial cell transformed with Wnt-1 whose expression is reduced or absent in the parental myoepithelial cell. The polyA RNA extracted from both types of cells was used to synthesize tester and driver cDNAs. The degree of subtraction efficiency was monitored by Southern blot analysis of unsubtracted and subtracted PCR products using a β-actin probe. No β-actin mRNA was apparent in the subtracted PCR products, confirming the efficiency of the subtraction.

The subtracted cDNA library was subcloned into a pGEM-T vector for further analysis. A random sample of 1996 clones was sequenced from the transformed colonies obtained. To determine if the clones obtained were differentially expressed, PCR primers were designed for selected clones and semi-quantitative RT-PCR and Northern analyses were performed using mRNA from the mouse mammary cell line and its derivative. It was found that expression of Wnt-1 in C57MG cells leads to elongated cell morphology and loss of contact inhibition.

One clone (m568.19A) of those that fulfilled the criteria for differential expression was found to encode full-length mouse WISP-1. By both RT-PCR analysis and Northern analysis, it was found that this clone provided an about three-fold induction in the Wnt-1 cell line over the parent cell line.

The cDNA sequence of this clone and deduced amino acid sequence of full-length mouse WISP-1 are shown in FIGS. 1A-1B (SEQ ID NOS:9 and 12, respectively) The sequence alignment of human and mouse WISP-1 (SEQ ID NOS:4 and 12, respectively) is shown in FIG. 8. In situ analysis of the clone is presented below, along with thymidine incorporation assay and angiostatic assay results.

This clone was placed in pRK5E, an E. coli-derived cloning vector having a human cytomegalovirus intermediate early gene promoter, an SV40 origin and polyA site, an sp6 transcription initiation site, a human immunoglobulin splice acceptor, and XhoI/NotI cDNA cloning sites. It is a progeny of pRK5D that has an added SceI site. Holmes et al., Science, 253:1278-1280 (1991). Upon transformation into JM109 cells, the plasmid rendered the cells ampicillin resistant. Upon digestion with XbaI and BamHI, a 1140-bp fragment was obtained, and the mouse insert size was 1122 base pairs, from the ATG to the stop codon, including a 3′ tag of six histidines.

Example 2 Isolation of a cDNA Clone Encoding Mouse WISP-2

The cDNA for mouse WISP-2 was isolated independently by Wnt-1 differential screening using the procedure described in Example 1. The initial clone isolated was 318 bp in length and was designated clone 1367. There were four clones in this cluster. The clone was sequenced as described above and RT-PCR primers were designed as follows: 1367.pcr.top1: nucleotides 1604-1627 of FIGS. 2A-2B: (SEQ ID NO:110) 3′-GGTGTGAAGACCGTCCGGTCCCGG and 1367.pcr.bot1: nucleotides 1438-1461 of FIGS. 2A-2B: (SEQ ID NO:111) 5′-GTGT(3CCTTTCCTGATCTGAGAAC After RT-PCR and Northern blot procedures were carried out as described in Example 1 to confirm differential expression, a five-fold induction in the Wnt-1 cell line was observed.

Clones encoding full-length mouse WISP-2 were isolated from RNA library 211: C57MG/Wnt-1. mRNA for construction of this library was isolated from the C57MG/Wnt-1 cell line described in Example 1. The RNA was used to generate an oligo-dT-primed cDNA library in the cloning vector pRK5E using reagents and protocols from Life Technologies, Gaithersburg, Md. (SUPERSCRIPT PLASMID SYSTEM™).

In this procedure, the double-stranded cDNA was primed with oligo dT containing a NotI site, linked with blunt-to-SalI hemikinased adaptors, cleaved with NotI, sized to greater than 1000 bp appropriately by gel electrophoresis, and cloned in a defined orientation into the XhoI/NotI-cleaved pRK5E vector. The library was screened by colony hybridization with a probe 1367.50mer.1 of bases 1463-1512 of FIGS. 2A-2B: 3′-GGGACGGGCCGACCCTTCTTAAAAGACCCTTGTACTTCTCTACCTTAGTG (SEQ ID NO:112). The full-length mouse WISP-2 clone was obtained, designated clone 1367.3.

The cDNA for mouse WISP-2, like the mouse WISP-1 molecule, encodes a novel secreted protein that belongs to the CTGF family and is the mouse homologue of SST DNA33473 of Example 4. (The alignment of human and mouse WISP-2 (SEQ ID NOS: 16 and 20, respectively) is shown in FIG. 9.) The mouse WISP-2 gene is 38% identical in sequence to mouse wisp-1, disclosed in Example 1, but lacks the C-terminal 95 amino acids thought to be involved in dimerization and receptor binding. Mouse WISP-2 was highly expressed in the lung. In-situ analysis of the clone is noted below. The nucleotide sequence and putative amino acid sequence of full-length mouse WISP-2 are shown in FIGS. 2A-2B (SEQ ID NOS:17 and 20, respectively). The putative signal sequence is from amino acid positions 1 to 23 of SEQ ID:20.

The clone was inserted into pRK5E, described above. Upon transformation of JM109 cells, the plasmid rendered the cells ampicillin resistant, Upon digestion with BamHI and NotI, a 1770-bp fragment was obtained, having a mouse insert of 756 bp from ATG to the stop codon.

Example 3 Isolation of a cDNA Clone Encoding Human WISP-1

To isolate the full-length human clone corresponding to m568.19A (mouse WISP-1), a human lung cDNA library (Clontech), treated with the SUPERSCRIPT™ kit using the pRKSE vector as described above, was screened with a 70-bp probe at low stringency (20% formamide, 1×SSC, 55° C. wash). The probe had the sequence from nucleotides 909-978 of the full-length mouse WISP-1 nucleotide sequence of FIGS. 1A-1B, i.e., the sequence: (SEQ ID NO:113) 51-CCAGCCAGAGGAGGCCACGAACTTCACTCTCGCAGGCTGTGTCAGCA CACGCACCTACCGACCCAAGTAC

Only one clone was identified, hL.568.15A. The insert to this clone was subcloned into pBLUESCRIPT™ IISK+ and its DNA sequence determined by dideoxy DNA sequencing on both strands. This clone was found to be missing about 280 amino acids. Hence, a new probe (hu.568.50mer.1) was designed from clone 15A having the nucleotides 750-799 of the full-length human WISP-1 nucleotide sequence shown in FIGS. 3A and 3B, i.e., (SEQ ID NO:114) 51-GCCCCTGGAGCCCTTGCTCCACCAGCTGCGGCCTGGGGGTCTCCACT CGG This probe was used to screen a human fetal kidney cDNA library (Clontech) treated with the SUPERSCRIPT™ kit using the pRK5E vector as described above, by colony hybridization. A number of clones were obtained by screening this human fetal kidney cDNA library (clones without the A or B designation) or by screening a human fetal kidney λgt10 library (clones with the A or B designation) using the same probes described above. The inserts of these clones were subcloned into PBLUESCRIPT™ IISK+ and their DNA sequences determined by dideoxy DNA sequencing on both strands.

Two of these clones, designated as 568.1A and 568.4A, have their respective sequences (SEQ ID NOS:24 and 26) shown in FIGS. 27 and 29. These clones are missing the von Willebrand C1 domain, the variable domain, and the thrombospondin 1 domain, and have a frameshift, other clones, designated as 568.13, 568.39, 568.5A, 568.6B, and 568.7 (SEQ ID NOS:23, 25, 27, 28, and 29, respectively; FIGS. 26, 28, and 30-32, respectively), were obtained that lack one or more domains and/or short amino-acid stretches (e.g., an 8-amino-acid deletion) or contain additional short amino-acid stretches and may contain introns or alternative splice variants.

Two clones sharing a significant amount of sequence with the full-length clone 568.38 were identified: 568.23 and 568.35. Human clone 568.38 encoded the full-length human WISP-1. The nucleotide sequence and putative amino acid sequence for clone 568.38 are shown in FIGS. 3A-3C (SEQ ID NOS:1 and 4, respectively). The aligning sequences of clones 568.38 and 568.35 differ from the corresponding aligning sequences of clones 568.15A and 568.23 in that the respective sequences of the latter two clones have an isoleucine residue at amino acid position 184 of FIGS. 3A-3C, whereas the respective corresponding sequences of clones 568.38 and 568.35 have a valine residue at this position. Further, the aligning sequences of clones 568.35 and 568.38 differ from each other in that the sequence of clone 568.35 has a serine residue at amino acid position 202 of FIGS. 3A-3C, whereas the corresponding sequence of clone 568.38 has an alanine residue at this position.

The human WISP-1 polypeptide, by homology searching, is also found to be a member of the CTGF family. The clone was placed in a pRK5E plasmid as described above and deposited with the ATCC. Upon transformation into JM109 cells, the plasmid rendered the cells ampicillin resistant. Digestion with ClaI and EcoRV yielded a 1435-bp fragment with an insert size of 1104 basepairs from ATG to the stop codon.

In situ hybridization of human WISP-1 was performed, with the results given below. Northern analysis of human WISP-1 showed high expression in adult heart tissue and ovary tissue, and in fetal kidney tissue. Also presented below are thymidine incorporation assay, gene amplification assay, and angiostatic assay results.

The chromosomal location of the human WISP genes was determined by radiation hybrid mapping using the Stanford G3™ and the MIT Genebridge 4 Radiation Hybrid™ panels. WISP-1 resides at approximately 3.48 cR from the meiotic marker AFM259xc5 (LOD score 16.31) on the Genebridge map. This places WISP-1 in band 8q24.1 to 8q24.3, roughly four megabases distal to c-myc located at chromosome band 8q24.12-8q24.13. Takahashi et al., Cytogenet. Cell Genet., 57: 109-111 (1991). c-myc is a region that is a recurrent site of amplification in non-small cell lung carcinoma.

Example 4 Isolation of a cDNA Clone Encoding Human PR0261 (Designated Herein as Human WISP-2)

The extracellular domain (ECD) sequences (including the secretion signal, if any) of from about 950 known secreted proteins from the SWISS-PROT™ public protein database were used to search expressed sequence tag (EST) databases. The EST databases included public EST databases (e.g., GenBank) and a proprietary EST DNA database (LIFESEQ™, Incyte Pharmaceuticals. Palo Alto, Calif.). The search was performed using the computer program BLAST or BLAST2 (Altshul et al., Methods in Enzymology 266:460-480 (1996)) as a comparison of the ECD protein sequences to a 6-frame translation of the EST sequence. Those comparisons resulting in a BLAST score of 70 (or in some cases 90) or greater that did not encode known proteins were clustered and assembled into consensus DNA sequences with the program “phrap” (Phil Green, University of Washington, Seattle, Wash.: http://bozeman.mbt.washington.edu/phrap.docs/phrap.html).

A consensus DNA sequence was assembled relative to other EST sequences using phrap. The EST sequences used (from Incyte) were Nos. 2633736, 2118874, 360014, 2316216, 1985573, 2599326, 1544634, 2659601, 1319684, 783649, 627240, 1962606, 2369125, 939761, 1666205, 692911, 984510, 1985843, 2104709, and 2120142. This consensus sequence is herein designated DNA30843 (see FIG. 5). Based on the DNA30843 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PR0261 (human, WISP-2). A pair of PCR primers, forward and reverse, were synthesized having the respective sequences: (SEQ ID NO:115) 5′-AAAGGTGCGTACCCAGCTGTGCC and (SEQ ID NO:116) 3′-TCCAGTCGGCAGAAGCGGTTCTGG.

Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA30843 sequence, which probe has the sequence: (SEQ ID NO:117) 5′-CCTGGTGCTGGATGGCTGTGGCTGCTGCCGGGTATGTGCAGGGCGGG TGGG.

For screening several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification, as per Ausubel et al., Current Protocols in Molecular Biology (Green Publishing Associates and Wiley Interscience, N.Y., 1989), with the PCR primer pair identified above. A positive library was then screened by colony hybridization to isolate clones encoding PR0261 (human WISP-2) using the probe oligonucleotide and one of the PCR primers.

RNA for construction of the cDNA libraries was isolated from human fetal lung tissue. The cDNA libraries used to isolate the cDNA clones were constructed by standard methods using commercially available reagents such as those from Invitrogen, San Diego, Calif. The cDNA was primed with oligo dT containing a NotI site, linked with blunt-to-SalT-hemikinased adaptors, cleaved with NotI, sized appropriately by gel electrophoresis, and cloned in a defined orientation into a suitable cloning vector (such as pRK5B or pRK5D; pRK5B is a precursor of pRK5D that does not contain the SfiI site; see Holmes et al., Science, 253:1278-1280 (1991)) in the unique XhoI and NotI sites.

DNA sequencing of the clones isolated as described above gave the DNA sequence for PR0261 (herein designated as UNQ228 (DNA33473-seq min); SEQ ID NO:38), which begins at nucleotide 34 of SEQ ID NO:13 (FIG. 4A-4B) and the derived amino acid sequence for PR0261 (SEQ ID NO:16).

The entire nucleotide sequence encoding human WISP-2 is shown in FIGS. 4A-4B (SEQ ID NO:13). This sequence contains a single open reading frame with an apparent translational initiation site at nucleotide positions 22-24 of SEQ ID NO:13 and ending at the stop codon after nucleotide 770 of SEQ ID NO:13 (FIGS. 4A-4B). The predicted polypeptide precursor is 250 amino acids long (FIGS. 4A-4B). The putative signal sequence spans from amino acid positions 1 to 23 of SEQ ID NO:16. Clone UNQ228 (DNA33473-seq min) has been deposited with ATCC and is assigned ATCC deposit no. 209391.

Analysis of the amino acid sequence of the full-length PR0261 polypeptide suggests that portions of it possess significant homology to CTGF, thereby indicating that PR0261 is a novel growth factor.

The entire nucleotide sequence encoding human WISP-3 from this clone is shown in FIGS. 6A-6C (SEQ ID NO:30) This sequence contains a single open reading frame with an apparent translational initiation site at nucleotide positions 46-48 of SEQ ID NO:30 and ending at the stop codon after nucleotide 1161 of SEQ ID NO:30 (FIGS. 6A-6C). The predicted polypeptide precursor is 372 amino acids long (FIGS. 6A-6C). The putative signal sequence is from amino acid positions 1 to 33 of SEQ ID NO:33. Clone UNQ462 (DNA56350-1176-2) has been deposited with ATCC and is assigned ATCC deposit no. 209706.

Example 5 Isolation of cDNA Clones Encoding Human WISP-3

In this example, the gene encoding WISP-3 was cloned twice essentially in parallel. First, it was determined whether the databases described above contained any new members of the WISP family. Two EST homologies to the WISPs were found and both were cloned. Full-length clones were isolated corresponding to each of these EST homologies. The efforts resulted in two full-length clones of the same gene (the original EST homologies had been from distinct regions of the same gene). The first clone obtained was designated as DNA56350 and the second as DNA58800.

DNA56350

Based on the sequence of INCYTE 3208053, a virtual DNA 48917 was obtained and oligonucleotides were synthesized for use as probes to isolate a clone of the full-length coding sequence for PRO956 (human WISP-3). A pair of PCR primers, forward and reverse, were synthesized having the sequences: (SEQ ID NO:118) 5′-GTCTTGTGCAAGCAACAAAATGGACTCC (SEQ ID NO:119) 3′-GACACAATGTAAGTCGGAACGCTGTCG

Additionally, a synthetic oligonucleotide hybridization probe was constructed from the INCYTE sequence, which probe has the sequence: (SEQ ID NO:120) 5′-GCTCCAGAACATGTGGGATGGGAATATCTAACAGGGTGACCAATGAA AAC

A human fetal kidney library primed with oligo dT containing a XhoI-NotI size cut greater than 3700 kb was screened for a source of a full-length clone by PCR amplification with the PCR primer pair identified above. The positive library was then used to isolate clones encoding PR0956 (human WISP-3) using the probe oligonucleotide and one of the PCR primers.

DNA sequencing of the clone isolated as described above gave the DNA sequence for PR0956 (herein designated as UNQ462 (SEQ ID NO:30), and the derived amino acid sequence for PR0956 (SEQ ID NO:33).

The entire nucleotide sequence encoding human WISP-3 from this clone is shown in FIG. 6 (SEQ ID NO:30). This sequence contains a single open reading frame with an apparent translational initiation site at nucleotide positions 46-48 of SEQ ID NO:30 and ending at the stop codon after nucleotide 1161 of SEQ ID NO:30 (FIG. 6). The predicted polypeptide precursor is 372 amino acids long (FIG. 6). The putative signal sequence is from amino acid positions 1 to 33 of SEQ ID NO:33. Clone UNQ462 (DNA56350-1176-2) has been deposited with ATCC and is assigned ATCC deposit no. 209706.

Analysis of the amino acid sequence of the full-length PR0956 polypeptide suggests that portions of it possess significant homology to CTGF, thereby indicating that PRO956 is a novel growth factor. This, clone has an additional methionine just 5′ of the first methionine in this clone. The amino acid sequence of this clone is 42% homologous to that of human WISP-1, and 32% homologous to that of human WISP-2.

In situ hybridization of human WISP-3 is shown below. Using the mapping techniques set forth above, it was found that human WISP-3 was localized to chromosome 6q22-6q23 and was linked to the marker AFM211ze5 with a LOD score of 1000. WISP-3 is approximately 18 megabases proximal to CTGF and 23 megabases promimal to the human cellular oncogene MYB, which are also located at 6q22-6q23. Martinerie et al., Oncogene, 7: 2529-2534 (1992); Meese et al., Genes Chromosomes Cancer, 1: 88-94 (1989).

The clone was inserted into pRK5E, described above. Upon transformation of JM109 cells, the plasmid rendered the cells ampicillin resistant. Upon digestion with BamHI and NotI, a fragment was obtained having a human insert from ATG to the stop codon as indicated in FIG. 6.

DNA58800

Based on the sequence of HS142L7, a virtual DNA 56506 was obtained and oligonucleotides were synthesized for use as probes to isolate a clone of the full-length coding sequence for PR0790 (human WISP-3). To this end, a pair of PCR primers, forward and reverse, were synthesized having the sequences: (SEQ ID NO:121) 5′-CCTGGAGTGAGCCTGGTGAGAGA (SEQ ID NO:122) 3′-ACACTGGGTGTGTTTCCCGACATAACA

Additionally, a synthetic oligonucleotide hybridization probe was constructed from the HS 142L7 sequence, which probe has the sequence: (SEQ ID NO:123) 5′-TGGTTGCTTGGCACAGATTTTACAGCATCCACAGCCATCTCTCA

A human bone marrow library primed with oligo dT containing a XhoI-NotI size cut of 1-3 kb was screened for a source of a full-length clone by PCR amplification with the PCR primer pair identified above. The positive library was then used to isolate clones encoding PR0790 (human WISP-3) using the probe oligonucleotide and one of the PCR primers.

DNA sequencing of the clone isolated as described above gave the DNA sequence for PRO790 (SEQ ID NO:34), and the derived amino acid sequence for PR0790 (SEQ ID NO:37).

The entire nucleotide sequence encoding human WISP-3 from this clone is shown in FIGS. 7A-7C (SEQ ID NO:34). This sequence contains a single open reading frame with an apparent translational initiation site at nucleotide positions 16-18 of SEQ ID NO:34 and ending at the stop codon after nucleotide 1077 of SEQ ID NO:34 (FIGS. 7A-7C). The predicted polypeptide precursor is 355 amino acids long (FIGS. 7A-7C). The putative signal sequence spans from amino acid positions 1 to 15 of SEQ ID NO:37. This clone DNA58800-1176-2 has been deposited with ATCC and is assigned ATCC deposit no. 209707.

Analysis of the amino acid sequence of the full-length PRO790 polypeptide suggests that portions of it possess significant homology to CTGF, thereby indicating that, like PRO956 which is a splice variant thereof, PR0790 is a novel growth factor.

In situ hybridization of human WISP-3 is shown below.

The clone was inserted into pRK5E, described above. Upon transformation of JM109 cells, the plasmid rendered the cells ampicillin resistant. Upon digestion with BamHI and NotI, a fragment was obtained having a human insert from ATG to the stop codon as indicated in FIGS. 7A-7C.

Example 6 Use of WISP-Encoding DNA as a Hybridization Probe

The following method describes use of a nucleotide sequence encoding a WISP polypeptide as a hybridization probe.

DNA comprising the coding sequence of full-length or mature human WISP-1 (as shown in FIGS. 3A-3C, SEQ ID NOS:4 or 3, respectively), or full-length or mature mouse WISP-1 (as shown in FIGS. 1A-1B, SEQ ID NOS:12 or 11, respectively), or of full-length or putative mature human WISP-2 (as shown in FIG. 4A-4B, SEQ ID NOS:16 or 15, respectively), or full-length or putative mature mouse WISP-2 (as shown in FIGS. 2A-2B, SEQ ID NOS:20 or 19, respectively) is employed as a probe to screen for homologous DNAs (such as those encoding naturally occurring variants of these particular WISP proteins in human tissue cDNA libraries or human tissue genomic libraries.

Hybridization and washing of filters containing either library DNAs is performed under the following high-stringency conditions. Hybridization of radiolabeled WIS P-polypeptide-derived probe (such as UNQ228 (DNA33473-seq min)-derived probe) to the filters is performed in a solution of 50% formamide, 5×SSC, 0.1% SDS, 0.1% sodium pyrophosphate, 50 mM sodium phosphate, pH 6.8, 2×Denhardt's solution, and 10% dextran sulfate at 42° C. for 20 hours. Washing of the filters is performed in an aqueous solution of 0.1×SSC and 0.1% SDS at 42° C.

DNAs having a desired sequence identity with the DNA encoding a full-length, native-sequence WISP polypeptide can then be identified using standard techniques known in the art.

Example 7 Expression of WISP Polypeptide in E. coli

This example illustrates preparation of an unglycosylated form of WISP polypeptide by recombinant expression in E. coli.

The DNA sequence encoding WISP polypeptide is initially amplified using selected PCR primers. The primers should contain restriction enzyme sites which correspond to the restriction enzyme sites on the selected expression vector. A variety of expression vectors may be employed. An example of a suitable vector is pBR322 (derived from E. coli; see Bolivar et al., Gene, 2: 95 (1977)) which contains genes for ampicillin and tetracycline resistance. The vector is digested with restriction enzyme and dephosphorylated. The PCR-amplified sequences are then ligated into the vector. The vector will preferably include sequences which encode an antibiotic-resistance gene, a trp promoter, a polyhis leader (including the first six STII codons, polyhis sequence, and enterokinase cleavage site), the WISP-coding region, lambda transcriptional terminator, and an argU gene.

The ligation mixture is then used to transform a selected E. coli strain using the methods described in Sambrook et al., supra. Transformants are identified by their ability to grow on LB plates, and antibiotic-resistant colonies are then selected. Plasmid DNA can be isolated and confirmed by restriction analysis and DNA sequencing.

Selected clones can be grown overnight in liquid culture medium such as LB broth supplemented with antibiotics. The overnight culture may subsequently be used to inoculate a larger-scale culture. The cells are then grown to a desired optical density, during which the expression promoter is turned on.

After the cells are cultured for several more hours, the cells can be harvested by centrifugation. The cell pellet obtained by the centrifugation can be solubilized using various agents known in the art, and the WISP polypeptide can then be purified using a metal-chelating column under conditions that allow tight binding of the protein.

Example 8 Expression of WISP Polypeptide in Mammalian Cells

This example illustrates preparation of a potentially glycosylated form of WISI-polypeptide by recombinant expression in mammalian cells.

The vector, pRK5E, was employed as the expression vector. The appropriate DNA encoding WISP polypeptide was ligated into pRK5E with selected restriction enzymes to allow insertion of the DNA for WISP polypeptide using ligation methods as described in Sambrook et al., supra. The resulting vectors were pRK5E.h.WIG-1.568.38, pRK5E.m.WIG-1.568.6his, pRK5E-m.WIG-2.1367.3, plasmid encoding human WISP-2, DNA56350-1176-2, and DNA58800-1176-2, all deposited at the ATCC. These vectors are conveniently referred to collectively as pRK5E.WISP in the general description below.

In one embodiment, the selected host cells may be 293 cells. Human 293 cells (ATCC CCL 1573) are grown to confluence in tissue culture plates in medium such as DMEM supplemented with fetal calf serum and optionally, nutrient components and/or antibiotics. About 10 αg pRK5E.WISP DNA is mixed with about 1 μg DNA encoding the VA RNA gene (Thimmappaya et al., Cell, 31:543 (1982)) and dissolved in 500 μl of 1 mM Tris-HCl, 0.1 mM EDTA, 0.227 M CaCl₂. To this mixture is added, dropwise, 500 μl of 50 mM HEPES (pH 7.35), 280 mM NaCl, 1.5 MM NaPO₄, and a precipitate is allowed to form for 10 minutes at 25° C. The precipitate is suspended and added to the 293 cells and allowed to settle for about four hours at 37° C. The culture medium is aspirated off and 2 ml of 20% glycerol in phosphate-buffered saline (PBS) is added for 30 seconds. The 293 cells are then washed with serum-free medium, fresh medium is added, and the cells are incubated for about 5 days.

Approximately 24 hours after the transfections, the culture medium is removed and replaced with culture medium (alone) or culture medium containing 200 μCi/ml ³⁵S-cysteine and 200 μCi/Ml ³⁵S-methionine. After a 12-hour incubation, the conditioned medium is collected, concentrated on a spin filter, and loaded onto a 15% SDS gel. The processed gel may be dried and exposed to film for a selected period of time to reveal the presence of the WISP polypeptide. The cultures containing transfected cells may undergo further incubation (in serum-free medium) and the medium is tested in selected bioassays.

In an alternative technique, the WISP polypeptide may be introduced into 293 cells transiently using the dextran sulfate method described by Somparyrac et al., Proc. Natl. Acad. Sci., 12:7575 (1981). 293 cells are grown to maximal density in a spinner flask and 700 μg pRK5E.WISP DNA is added. The cells are first concentrated from the spinner flask by centrifugation and washed with PBS. The DNA-dextran precipitate is incubated on the cell pellet for four hours. The cells are treated with 20% glycerol for 90 seconds, washed with tissue culture medium, and re-introduced into the spinner flask containing tissue culture medium, 5 μg/ml bovine insulin, and 0.1 μg/ml bovine transferrin. After about four days, the conditioned media are centrifuged and filtered to remove cells and debris. The sample containing expressed WISP polypeptide can then be concentrated and purified by any selected method, such as dialysis and/or column chromatography.

In another embodiment, the WISP polypeptide can be expressed in CHO cells. The pRK5E.WISP can be transfected into CHO cells using known reagents such as CaPO₄ or DEAE-dextran. As described above, the cell cultures can be incubated, and the medium replaced with culture medium (alone) or medium containing a radiolabel such as ³⁵S-methionine. After determining the presence of the WISP polypeptide, the culture medium may be replaced with serum-free medium. Preferably, the cultures are incubated for about 6 days, and then the conditioned medium is harvested. The medium containing the expressed WISP polypeptide can then be concentrated and purified by any selected method.

Epitope-tagged WISP polypeptide may also be expressed in host CHO cells. The WISP polypeptide may be subcloned out of the pRK5 vector. Suva et al., Science, 237: 893-896 (1987) EP 307,247 published Mar. 15, 1989. The subclone insert can undergo PCR to fuse in-frame with a selected epitope tag such as a poly-his tag into a baculovirus expression vector. The poly-his-tagged WISP polypeptide insert can then be subcloned into a SV40-driven vector containing a selection marker such as DHFR for selection of stable clones. Finally, the CHO cells can be transfected (as described above) with the SV40-driven vector. Labeling may be performed, as described above, to verify expression. The culture medium containing the expressed poly-His-tagged WISP can then be concentrated and purified by any selected method, such as by Ni²⁺-chelate affinity chromatography.

In particular, mouse WISP-1 cDNA for insertion into mammalian expression vectors was created via PCR using clone m568.19A (see above) pure phage DNA as template and using as primers m.568.pcr.top4 (5′-TGACTTCCAGGCATGAGGTGGCTCCTG; SEQ ID NO:124) and m.568.pcr.bot3 (5′-ATTGGCAATCTCTTCGAAGTCAGGGTAAGATTCC; SEQ ID NO:125) for the 6-his version, or m.568.pcr.top4 (SEQ ID NO:124) and 568.pcr.bot5, which has a 3′-terminal XbaI site (5′-GGTACGTCTAGACTAATTGGCAATCTCTTCGAAGTCAGGG; SEQ ID NO:126) for the non-his version. The insert integrity was confirmed by sequencing and analyzed. The PCR was run using Pfu polymerase and the conditions were: temp. time denaturation 94° C.   1 min annealing 62° C.  30 sec extension 72° C. 1.5 min # of cycles: 25

For transient expression in 293 cells analyzed by Western blot, the above inserts were ligated into the pRK5 vector referred to above at the BamHI/XbaI site using the BOEHRINGER MANNHEIM™ rapid ligation kit. The resulting plasmids were designated pRK5.mu.WISP-1.6his and pRK5.mu.WISP-1.nohis for the His-tagged and non-His-tagged inserts, respectively. Then the 293 cells were plated and allowed to reach approximately 85% confluency overnight (37° C./5% CO₂). The plated cells were transfected with plasmid DNA pRK5.mu.WISP-1.6his or pRK5.mu.WISP-1.nohis by using lipofectamine (Gibco BRL) at a 4.5:1 lipid:DNA ratio.

Transfection efficiency (>70% usually) was monitored using a GFP expression plasmid (pGREEN LANTERN™ from Gibco BRL). Approximately 5 hours post-transfection, the medium was changed to fresh SF media (50:50 with 1×L-Glu and 1×P/S) for protein production. The conditioned media was allowed to accumulate for specified amounts of time (depending on the experiment) before harvesting.

The medium was harvested and concentrated in the presence of 1 mM PMSF using the CENTRICON-10™ concentrator. The concentrated, conditioned media (usually 1.5 ml) was then bound to Ni-⁺⁺ NTA agarose beads (Qiagen) for 2 hours (for the His-tagged version only). Protein was eluted from the beads by boiling for 10 minutes in 2×SDS loading buffer (Novex) with or without beta-mercaptoethanol for reduced vs. non-reduced protein, respectively.

The protein was visualized by SDS-PAGE using 4-20% gradient TRIS-glycine gels, 10-wells, 1 mm thickness (Novex). Gels ran at 125 volts (constant) for 95 minutes. Western transfer was achieved using a NOVEX™ transfer apparatus to PVDF membranes (Novex) at 200 mA (constant) for 45 minutes. The blots were blocked for a minimum of 1 hour at room temperature in blocking buffer (PBS+TWEEN-20™ (0.5%), 5% dry milk, and 3% goat serum). Blots were incubated in primary antibody (for His-tagged protein: INVITROGEN™ anti-his (C-terminal)-HRP-conjugated antibody or for the non-His version: polyclonal anti-murine WISP-1 antibody prepared as described below) at a 1:2000 dilution in fresh blocking buffer for 1 hour at room temperature. The non-His-tagged protein blots were incubated in secondary antibody (PIERCE™ goat anti-rabbit IgG(H+L) HRP conjugated) diluted 1:2000 in fresh blocking buffer. The blots were incubated in chemiluminescent substrate (ECL™ from Amersham or SUPERSIGNAL™ from Pierce) for 1 minute before exposing to film.

For transient expression analyzed by antibody staining, 293 cells were cultured, plated, and transfected as described above. The cells were fixed to culture dishes for 2 minutes in 1:1 methanol:acetone solution. Fixed cells were then incubated in primary antibody (for His-tagged protein: INVITROGEN™ anti-his (C-term)-HRP-conjugated antibody or for the non-His version: polyclonal anti-murine WISP-1 antibody prepared as described below) diluted 1:1000 in PBS with 10% fetal bovine serum for 2 hours. The non-His-tagged protein blots were then incubated in secondary antibody (PIERCE™ goat anti-rabbit IgG(H+L) HRP conjugated) diluted 1:150 in PBS with 10% fetal bovine serum for 1 hour. The P incubation was in color reagent substrate for HRP for up to 1 hour (1.0% O-dianisidine-saturated ETOH, 0.01% hydrogen peroxide in PBS).

For stable expression of mouse WISP-1 in mammalian cells, the starting vector employed was pRK5.CMV.puro-dhfR, the sequence of which is shown in FIGS. 16A-16D. This vector has two SAR sequences cloned into KpnI, SapI sites of the SVIDS, splice-donor vector, and has the pSVI backbone with the pRK5 cloning linker (pSV15) and the intron made from pSVI.WTSD.D by adding a linearization linker ML) into the HpaI site. The sequence is edited to include changes in vector puc 118 backbone derived from the sequence of pRK5 and includes a four-base insertion after MCS characteristic of the SVI vector.

The above inserts were ligated into pRK5.CMV.puro-dhfR at the BamHI/XbaI site using the BOEHRINGER MANNHEIM™ rapid ligation kit, producing pRK5.CMV.puro-dhfR.mu.WISP-1.6his or pRK5.CMV.puro-dhfr.mu.WISP-1.nohis. This construct allows for stable selection of expressing cells using either puromycin (2 μg/ml in 293 cells or 10 μg/ml in CHO-DP12 cells) or the DHFR deletion in the CHO-DP12 line, which allows for subsequent amplification in methotrexate. Isolated colonies representative of stably transfected cells were picked, cultured under selective pressure, and analyzed by antibody staining or Western blot as described above.

Example 9 Expression of WISP Polypeptide in Yeast

The following method describes recombinant expression of a WISP polypeptide in yeast.

First, yeast expression vectors are constructed for intracellular production or secretion of a WISP polypeptide from the ADH2/GAPDH promoter. DNA encoding a WISP polypeptide and the promoter is inserted into suitable restriction enzyme sites in the selected plasmid to direct intracellular expression. For secretion, DNA encoding a WISP polypeptide can be cloned into the selected plasmid, together with DNA encoding the ADH2/GAPDH promoter, a native WISP signal peptide or other mammalian signal peptide or yeast alpha-factor or invertase secretory signal/leader sequence, and linker sequences (if needed) for expression.

Yeast cells, such as yeast strain AB110, can then be transformed with the expression plasmids described above and cultured in selected fermentation media. The transformed yeast supernatants can be analyzed by precipitation with 10% trichloroacetic acid and separation by SDS-PAGE, followed by staining of the gels with Coomassie Blue stain.

Recombinant WISP polypeptide can subsequently be isolated and purified by removing the yeast cells from the fermentation medium by centrifugation and then concentrating the medium using selected cartridge filters. The concentrate containing the WISP polypeptide may further be purified using selected column chromatography resins.

Example 10 Expression of WISP Polypeptide in Baculovirus-Infected Insect Cells and Purification Thereof

The following method describes recombinant expression of a WISP polypeptide in baculovirus-infected insect cells, and purification thereof.

General

The sequence coding for WISP polypeptide is fused upstream of an epitope tag contained within a baculovirus expression vector. Such epitope tags include poly-His tags and immunoglobulin tags (like Fc regions of IgG). A variety of plasmids may be employed, including plasmids derived from commercially available plasmids such as pVL1393 (Novagen). Briefly, the sequence encoding WISP polypeptide or the desired portion of the coding sequence (such as the sequence encoding the mature protein if the protein is extracellular) is amplified by PCR with primers complementary to the 5′ and 3′ regions. The 5′ primer may incorporate flanking (selected) restriction enzyme sites. The product is then digested with those selected restriction enzymes and subcloned into the expression vector.

Recombinant baculovirus is generated by co-transfecting the above plasmid and BACULOGOLD™ virus DNA (Pharmingen) into Spodoptera frugiperda (“Sf9”) cells (ATCC CRL 1711) using lipofectin (commercially available from Gibco-BRL). After 4-5 days of incubation at 28° C., the released viruses are harvested and used for further amplifications, viral infection and protein expression are performed as described by O'Reilley et al., Baculovirus Expression Vectors: A Laboratory Manual (oxford: Oxford University Press, 1994).

Expressed poly-His-tagged WISP polypeptide can then be purified, for example, by Ni²⁻-chelate affinity chromatography as follows. Extracts are prepared from recombinant virus-infected Sf9 cells as described by Rupert et al., Nature, 362:175-179 (1993). Briefly, Sf9 cells are washed, resuspended in sonication buffer (25 mL HEPES, pH 7.9; 12.5 mm MgCl₂; 0.1 mM EDTA; 10% glycerol; 0.1% NP-40; 0.4 M KCl), and sonicated twice for 20 seconds on ice. The sonicates are cleared by centrifugation, and the supernatant is diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCl, 10% glycerol, pH 7.8), and filtered through a 0.45 μm filter. A Ni²⁻-NTA agarose column (commercially available from Qiagen) is prepared with a bed volume of 5 mL, washed with 25 mL of water, and equilibrated with 25 mL of loading buffer. The filtered cell extract is loaded onto the column at 0.5 mL per minute. The column is washed to baseline A₂₈₀ with loading buffer, at which point fraction collection is started. Next, the column is washed with a secondary wash buffer (50 mM phosphate; 300 mM NaCl, 10% glycerol, pH 6.0), which elutes non-specifically bound protein. After reaching A₂₈₀ baseline again, the column is developed with a 0 to 500 mM imidazole gradient in the secondary wash buffer. One-mL fractions are collected and analyzed by SDS-PAGE and silver staining or Western blot with Ni²⁺-NTA-conjugated to alkaline phosphatase (Qiagen). Fractions containing the eluted His₁₀-tagged WISP polypeptide are pooled and dialyzed against loading buffer.

Alternatively, purification of the IgG-tagged (or Fc-tagged) WISP polypeptide can be performed using known chromatography techniques, including, for instance, Protein A or protein G column chromatography.

Specific

1. Expression

In particular, mouse WISP-1 polypeptide was expressed in a baculovirus expression system similar to that described above using as the baculovirus transfer vector pb.PH.mu.568.9.IgG.baculo or pbPH.mu.568.8his.baculo. FIGS. 17A-17D show the sequence (SEQ ID NO:54) of plasmid pb.PH.IgG, which was used to prepare pb.PH.mu.568.9.IgG.baculo. FIGS. 18A-18D show the sequence (SEQ ID NO:55) of plasmid pbPH.His.c, which was used to prepare pbPH.mu.568.8his.baculo.

Both of these baculovirus transfer vectors are based on pVL1393 (Pharmingen), which has neither the His nor Fc tags. The pb.PH.IgG vector (FIG. 17) allows the expression of foreign proteins under control of the AcNPV polyhedrin promoter, which is active in the very late phase of virus infection. The foreign protein can be expressed as a C-terminal human IgG fusicn protein. The His(b)-tag will not be translated as a result of the IgG stop coc'-.on just 51 of the His(8)-tag. The sequence encoding the foreign protein should Le inserted as a 3′ blunt-ended fragment into the unique StuI site preceeding the His-taq. In that case an additional proline residue will be added. The 5′ site can be either BamHI, EcoRI, NotI, NcoI, and NheI.

The IgG vector was constructed by NdeI digestion of the pVL1393.IgG plasmid followed by Klenow treatment to fill in the sticky end site. This is followed by a NcoI digest and insertion into the pbPH.His.c×NcoI/SmaI-digested vector.

The sequence of pbPH.His.c shown in FIGS. 18A-18D contains the backbone sequence of the vector pVL1392, which contains approximately the EcoRI/XmaIII fragment of AcMNPV C-6, from position 0.0 to 5.7 mu. Possee et al., Virology, 185: 229-241 (1991). It allows the expression of foreign proteins under control of the Autographa californica nuclear polyhedrosis virus (AcNPV) polyhedrin gene promoter, which is active in the very late phase of virus infection.

The foreign protein can be expressed as a C-terminally His- or a IgG (Fc region only)-tagged protein. The sequence encoding the foreign protein should be inserted as a 31-blunt-ended fragment into the unique SmaI site preceding the His-tag or the SluI site for IgG. In that case an additional glycine residue will be added for His tags and a proline will be added for IgG tags. The 5′ site can be either BamHI, NotI, EcoRI, or NcoI. BamHI was used for both.

The vectors were constructed by inserting a PCR insert into BamHIISmaI for the His vector and BamHIIStuj for the IgG vector. The PCR insert was made using 5′-phosphorylated primers as follows: m.568.pcr.top6 (5′-TTTCCCTTTGGATCCTAAACCAACATGAGGTGGCTCCTGCCC; SEQ ID NO:127) and m.568.pcr.bot3 (SEQ ID NO:125), 5′ phosphorylated. A twenty-cycle PCR reaction with Pfu polymerase enzyme was performed using the following conditions: 1 min at 95° C., 30 sec at 60° C., 3.5 min at 72° C. The PCR product was purified with QIAQUICK™ and digested with BamHI at 37° C. for 1 hr. The digested PCR insert was ligated into the digested vector using a 1:3 ratio of insert to vector with 1 pl T4 DNA ligase (Bio Labs). ULTRA MAX™ DH5a FT competent cells, 100 pl, (Gibco BRL Cat #10643-013) were added to the ligation product, and the mixture was incubated on ice for 30 min, followed by a heat shock at 42° C. for 45 sec. Individual colonies were picked and miniscreen DNA was prepared using QIA PREpTl (Qiagen). Construct sequencing was performed using ABI Prism's dRHODAMINE DYE™ terminator cycle sequencing.

The plasmid pb.PH.IgG has a polylinker BamHI-NotI-EcoRI-NcfI-SrfI-StuI-(IgG Fc region only)-Stop-XbaI-SpeI-PslI-BglII. The location of particular regions in this plasmid is as follows: Insertion of polylinker/foreign gene: 4129-4912 (BamHI-BglII), polh coding: 4913-5479, ORF 1629: 7134-4820; ORF 588 (PK1): 7133-7723; ColEI origin of replication: −7973-8858, and ampicillin coding: 9779-8230. The plasmid pbPH.His.c has a polylinker BamHI-NotI-EcoRI-NcoI-SrfI-SmaI-(His 8)-Stop-XbaI-SpeI-PstI-BglII. The NcoI site of pbPH.His.c resides within a Kozak sequence. The location of particular regions in this plasmid is as follows: ORF 504 (PTP): 76-582, ORF 984 (ORF2): 1600-614, ORF 453 (ORF3): 2323-1868, conotoxin: 1818-1657, ORF 327 (ORF4): 2352-2681, ORF 630 (lef-2): 2662-3294, ORF 603: 3937-3332, ORF polh: 4093 (mutated codon ATG/′ATT), insertion of polylinker/foreign gene: 4129-4218 (BamHI-BglII), polh coding: 4224-4790, ORF 1629: 6445-4820, ORF 588 (PK1): 6444-7034, ColEI origin of replication: 7284-8169, and ampicillin coding:9090-8230.

The mouse WISP-1 cDNA disclosed herein was inserted into the vectors pbPH.His.c and pb.PH.IgG to produce the respective expression plasmids by creating a 3′ blunt-ended fragment for cloning into the unique SmaI site preceding the His-tag or IgG-tag. An additional glycine residue was added to the His protein produced. An additional proline was added to the IgG protein. The 51 site of the cDNA insert was BamHI.

2. Purification

For purification purposes, either a poly-His tag or the Fc portion of human IgG was added to the C-terminal coding region of the cDNA before expression. The conditioned media from the transfected cells (0.5 to 2 L) was harvested by centrifugation to remove the cells and filtered through 0.22 micron filters. For the poly-His-tagged constructs, the protein was purified using a Ni*2-NTA column (Qiagen). Before purification, imidazole was added to the conditioned media to a concentration of 5 mM. The conditioned media was pumped onto a 6-ml Ni*2-NTA column equilibrated in 20 mM HEPES, pH 7.4, buffer containing 0.3 M NaCl and 5 mM imidazole at a flow rate of 4-5 ml/min at 4° C. After loading, the column was washed with additional equilibration buffer and the protein was eluted with equilibration buffer containing 0.25 M imidazole. The highly purified protein was subsequently desalted into a storage buffer containing 10 MM HEPES, 0.14 M NaCl, and 4% mannitol, pH 6.8, with a 25 ml G25 SUPERFINE™ (Pharmacia) column and stored at −80° C.

Immunoadhesin (Fc-containing) constructs of WISP-1 protein were purified from the conditioned media as follows. The conditioned media was pumped onto a 5-ml Protein A column (Pharmacia) which had been equilibrated in a 20 mm Na phosphate buffer, pH 6.8. After loading, the column was washed extensively with equilibration buffer before elution with 100 mM citric acid, pH 3.5. The eluted protein was immediately neutralized by collecting 1-ml fractions into tubes containing 275 uL of 1 M Tris, pH 9, buffer. The highly purified protein was subsequently desalted into storage buffer as described above for the poly-His-tagged proteins. The homogeneity of the protein was assessed by SDS polyacrylamide gels and by N-terminal amino acid sequencing by Edman degradation.

Example 11 Axis Duplication Assay

Xenopus embryos were injected with human WISP-2 mRNA into either a presumptive ventral or presumptive dorsal vegetal blastomere at the 8- to 16-cell stage to overexpress locally the encoded protein and assay for its developmental effects. The methods used are described in Sokol et al., Cell, 67: 741-752 (1991).

More specifically, for synthesis of capped RNA, human WISP-2 and mouse Wnt-1 cDNAs were cloned into the pGEMHE vector (gift of Dr. Todd Evans, AECOM) to prepare pGEMHE.hu.WISP-2.8H and pGEMHE.mu.Wnt-1, respectively. The constructs were linearized at the 3′ end using the SphI restriction enzyme. Capped RNAs were synthesized using AMBION's T7 MESSAGEMACHINE™ RNA synthesis kit.

For obtaining mature oocytes, an adult female Xenopus laevis was injected with 200 I.U pregnant mare serum 3 days before use. The night before the experiment, the female frog was injected with 800 I.U of human chorionic gonadotropin. Fresh oocytes were squeezed from female frogs the next morning. In vitro fertilization of oocytes was performed by mixing oocytes with minced testes from a sacrificed male frog. Fertilized eggs were dejellied with 2% cysteine (pH 7.8) for 10 minutes. Dejellied eggs were washed once with distilled water and transferred to 0.1×Modified Barth's Solution (MBS) (Methods in Cell Biology, Volume 36, Xenopus laevis: Practical uses in Cell and Molecular Biology, Kay and Peng, Eds (New York: Academic Press, 1991)) with 5% Ficoll. Eggs were lined on injection trays which contained 0.1×MBS with 5% Ficoll for injection. After injection, embryos were kept in 0.1×MBS in an 18° C. incubator. Embryos were staged according to Nieuwkoop and Faber, Normal Table of Xenopus laevis: (Daudin)-(Amsterdam: North-Holland, 1967).

For animal cap assays, embryos were injected at the 2-cell stage with 1 ng of capped RNA, and animal caps were isolated at stage 8 and cultured in 1×MMR for another 24 hours for the RT-PCR assay. Total RNA was isolated from harvested animal caps using a RNEASy™ kit (Qiagen). RNA samples (approximately 1 Pg) were reverse transcribed using random hexamer and GIBCO:BRL SUPERSCRIPT JIT′ reverse transcriptase. The annealing temperature for the PCR reactions was 55° C. unless noted otherwise.

For axis duplication assays, embryos at the 8-cell stage were injected with 1 ng capped RNA at either the dorsal or ventral vegetal blastomere and incubated in 0.1×MBS for 72 hours.

The sequences of PCR primers used in this experiment were: (SEQ ID NO:128) EF-1a.U: 5′-CAGATTGGTGCTGGATATGC (SEQ ID NO:129) EF-1a.D: 5′-ACTGCCTTGATTACTCCTAC (SEQ ID NO:130) noggin.U: 5′-AGTTGCAGATGTGGCTCT (SEQ ID NO:131) noggin.D: 5′-AGTCCAAGAGTCTCAGCA (SEQ ID NO:132) goosecoid.U: 5′-ACAACTGGAAGCACTGGA (SEQ ID NO:133) goosecoid.D: 5′-TCTTATTCCAGAGGAACC (SEQ ID NO:134) cardiac-actin.U: 5′-TCCCTGTACGCTTCTGGTCGTA (SEQ ID NO:135) cardiac-actin.D: 5′-TCTCAAAGTCCAAAGCCACATA (SEQ ID NO:136) NCAM.U: 5′-CACAGTTCCAGCAAATAC (SEQ ID NO:137) NCAM.D: 5′-GGAATCAGGCGGTACAGT

It was found that human WISP-2 can partially induce axis duplication in this assay.

Example 12 Thymidine Incorporation Assay

In a (³H)-thymidine incorporation assay, 19 different cell lines, including RAG (renal adenocarcinoma, mouse) and NRK-49F (normal kidney fibroblasts, rat) cells, identified in Table I below, were plated in 96-well plates at 3×104 in HGDMEM with 10% serum. Twenty four hours after plating, the medium was changed to HGDMEM with 0.2% serum before adding the test proteins. WISP proteins were added to a final concentration of approximately 3.6 ng/ul. Serial dilutions were made in a total volume of 70 μl/well of fresh media. After 18 hr incubation at 37° C., 5 μCi/ml (³H)thymidine was added for 5 hrs. Medium was aspirated and cells were removed with 1× trypsin onto a GF/C filter using Packard's™ 96-well FILTERMATE 196™. The filters were dried and 40 μl of scintillation fluid was added for counting on a top count, microplate scintillation counter (Packard).

The results are shown in Table I: TABLE I IH-Thymidine Incorporation Assay Results mWISP-1- hWISP-1- hWISP-2- Cell line Type ATCC No. IgG IgG IgG HT-29 adenocarcinoma HTB-38 No change No change (human moderately well- colon) differentiated Wi-Dr adenocarcinoma CCL-218 No change No change (human colon) Calu-1 epidermoid HTB-54 inhibits ˜1.1x inhibits ˜1.2X (human carcinoma grade lung, III, metastasis to pleura Calu-6 anaplastic HTB-56 No change stimulates (human carcinoma, ˜1.4X lung) probably lung SK-MES-1 squamous HTB-58 No change No change (human carcinoma, pleural lung) effusion A549 carcinoma CCL-185 inhibits-1.5x inhibits ˜1.7X (human lung) H460 large cell HTB-177 inhibits ˜1.4X inhibits ˜1.3X (human carcinoma lung) SW900 squamous cell HTB-59 no change no change (human carcinoma lung) MRC5 normal diploid CCL-171 no change no change (human lung) IMR-90 normal diploid CCL-186 stimulates stimulates (human ˜1.1x ˜1.5X lung) Wnt-I myo-epithelial inhibits ˜2x C57 mg (mouse mammary gland) MLg lung stimulates ˜4X (mouse lung) LL/2 lung carcinoma inhibits ˜2x (mouse lung) JC (mouse carcinoma inhibits ˜2x inhibits ˜3x mammary gland) N MuMG normal stimulates ˜2X stimulates (mouse ˜1.4X mammary gland) NRK-49F normal fibroblast stimulates ˜3X stimulates (rat kidney) ˜3.5x RAG adenocarcinoma stimulates stimulates ˜3X stimulates ˜4X (mouse ˜4.5X kidney) NIH/3T3 fibroblast stimulates ˜3X (mouse embryo) UCLA-P3 inhibits ˜1.5x inhibits ˜2X (human lung)

It is seen that WISP-1 and WISP-2 exhibit both stimulatory and inhibitory effects on proliferation of normal and tumor cells, depending on the cell line employed.

Example 13 Preparation of Antibodies that Bind WISP Polypeptide

1. Polyclonal Antibodies

Polyclonal antisera were generated in female New Zealand White rabbits against murine WISP-1 and human WISP-2. The antigens used were proteins fused with histidine for murine WISP-1 and proteins fused with the Fc portion of IgG for human WISP-2. The same protocol was used for both proteins. Each protein was homogenized with Freund's complete adjuvant for the primary injection and with Freund's incomplete adjuvant for all subsequent boosts. For the primary immunization and the first boost, 3.3 μg per kg body weight was injected directly into the popliteal lymph nodes as described in Bennett et al., J. Biol. Chem., 266: 23060-23067 (1991) and “Production of Antibodies by Inoculation into Lymph Nodes” by Morton Sigel et al. in Methods in Enzymology, Vol. 93 (New York: Academic Press, 1983). For all subsequent boosts, 3.3 μg per kg body weight was injected into subcutaneous and intramuscular sites. Injections were done every 3 weeks with bleeds taken on the following two weeks.

2. Monoclonal Antibodies

Techniques for producing monoclonal antibodies that can specifically bind a WISP polypeptides are known in the art and are described, for instance, in Goding, supra. Immunogens that may be employed include purified WISP polypeptide, fusion proteins containing WISP polypeptide, and cells expressing recombinant WISP polypeptide on the cell surface. Selection of the immunogen can be made by the skilled artisan without undue experimentation.

Mice, such as Balb/c, are immunized with the WISP immunogen emulsified in complete Freund's adjuvant and injected subcutaneously or intraperitoneally in an amount from 1 to 100 micrograms. Alternatively, the immunogen is emulsified in MPL-TDM adjuvant (Ribi Immunochemical Research, Hamilton, Mont.) and injected into the animal's hind foot pads. The immunized mice are then boosted 10 to 12 days later with additional immunogen emulsified in the selected adjuvant. Thereafter, for several weeks, the mice may also be boosted with additional immunization injections. Serum samples may be periodically obtained from the mice by retro-orbital bleeding for testing in ELISA assays to detect antibodies to WISP polypeptide.

After a suitable antibody titer has been detected, the animals “positive” for antibodies can be injected with a final intravenous injection of a WISP polypeptide. Three to four days later, the mice are sacrificed and the spleen cells are harvested. The spleen cells are then fused (using 35% PEG) to a selected murine myeloma cell line such as P3X63AgU.1, available from ATCC, No. CRL 1597, or x63-AgB.653 (Kearney et al., J. Immunology, 123: 1548 (1979)). The fusions generate hybridoma cells which can then be plated in 96-well tissue culture plates containing HAT (hypoxanthine, aminopterin, and thymidine) medium to inhibit proliferation of non-fused cells, myeloma hybrids, and spleen cell hybrids.

The hybridoma cells will be screened in an ELISA for reactivity against a WISP polypeptide. Determination of “positive” hybridoma cells secreting the desired monoclonal antibodies against a WISP polypeptide is within the skill in the art.

The positive hybridoma cells can be injected intraperitoneally into syngeneic Balb/c mice to produce ascites containing the anti-WISP polypeptide monoclonal antibodies. Alternatively, the hybridoma cells can be grown in tissue culture flasks or roller bottles. Purification of the monoclonal antibodies produced in the ascites can be accomplished using ammonium sulfate precipitation, followed by gel-exclusion chromatography. Alternatively, affinity chromatography based upon binding of antibody to protein A or protein G can be employed.

Specifically, for each of the human WISP-1 antibodies, five female Balb-c mice were pre-bled and then injected via their hind foot pads with purified human WISP-1, tagged with the Fc portion of IgG and emulsified prior to injection in MPL-TDM adjuvant (Ribi Immunochemical Research, Hamilton, Mont.) in a 1:1 ratio of WISP antigen to adjuvant. The dosing schedule for the WISP-1 immunogen was as follows: Injection Date- Dose/Site Dose/Animal Concentration Day 16 of month 1 50 μl site 100 μl/animal 6 μg/animal Day 12 of month 2 50 μl/site 100 μl/animal 6 μg/animal Day 21 of month 2 50 μl/site 100 μl/animal 6 μg/animal Day 28 of month 2 50 μl/site 100 μl/animal 2 μg/animal Day 4 of month 3 50 μl/site 100 μl/animal 2 μg/animal Day 11 of month 3 50 μl/site 100 μl/animal 2 μg/animal Day 18 of month 3 50 μl/site 100 μl/animal 2 μg/animal Day 25 of month 3 50 μl/site 100 μl/animal 2 μg/animal

For WISP-1, the mice were bled on Day 10 of month 4. After the mice were bled, the monoclonal antibodies were made by harvesting their spleens and by fusion as indicated above, using as the murine myeloma cell line X63.AgB.653.

The five monoclonal antibodies generated to human WISP-1 are: 10F2.2A7 gamma2b/kappa 10A9.2B1 gamma2a/kappa 8F7.1B1 gamma1/kappa 1H1.ID5 gamma1/kappa 2G7.2H4 gamma1/kappa

For WISP-2 monoclonal antibodies the same regimen is employed except that purified human WISP-2 is used as immunogen in the above protocol rather than purified human WISP-1 and the dosing schedule for the WISP-2 immunogen is as follows: Injection Date- Dose/Site Dose/Animal Concentration Day 16 of month 1 50 μl/site 100 μl/animal 6 μg/animal Day 21 of month 2 50 μl/site 100 μl/animal 1 μg/animal Day 28 of month 2 50 μl/site 100 μl/animal 1 μg/animal Day 4 of month 3 50 μl/site 100 μl/animal 1 μg/animal Day 11 of month 3 50 μl/site 100 μl/animal 1 μg/animal Day 18 of month 3 50 μl/site 100 μl/animal 1 μg/animal Day 25 of month 3 50 μl/site 100 μl/animal 1 μg/animal

Example 14 Uses of Antibodies that Bind WISP Polypeptide

1. Cell Lines

The established human breast tumor cells BT474 and MDA-MB-231 (which are available from ATCC) are grown in minimum essential medium (Gibco, Grand Island, N.Y.) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (HyClone, Logan, Utah), sodium pyruvate, L-glutamine (2 mM), non-essential amino acids, and 2× vitamin solution and maintained at 37° C. in 5% CO₂. Zhang et al., Invas. & Metas., 11:204-215 (1991); Price et al., Cancer Res., 50:717-721 (1990).

2. Antibodies

Anti-WISP-1 or anti-WISP-2 monoclonal antibodies that may be prepared as described above are harvested with PBS containing 25 mM EDTA and used to immunize BALB/c mice. The mice are given injections i.p. of 107 cells in 0.5 ml PBS on weeks 0, 2, 5 and 7. The mice with antisera that immunoprecipitated 32p-labeled Wnt-1 are given i.p. injections of a wheatgerm agglutinin-SEPHAROSE™ (WGA)-purified Wnt membrane extract on weeks 9 and 13. This is followed by an i.v. injection of 0.1 ml of the Wnt-1 preparation, and the splenocytes are fused with mouse myeloma line X63-Ag8.653. Hybridoma supernatants are screened for Wnt-1 binding by ELISA and radioimmunoprecipitation. MOPC-21 (IgG1) (Cappell, Durham, N.C.) is used as an isotype-matched control.

Additionally, the anti-ErbB2 IgG₁κ murine monoclonal antibodies 4D5 (ATCC CRL 10463 deposited May 24, 1990) and 7C2, specific for the extracellular domain of ErbB2, may be used with the above antibodies. They are produced as described in Fendly et al., Cancer Research, 50:1550-1558 (1990) and WO89/06692.

3. Analysis of Cell Cycle Status and Viability

Cells are simultaneously examined for viability and cell cycle status by flow cytometry on a FACSTAR PLUS™ (Becton Dickinson Immunocytometry Systems USA, San Jose, Calif.). Breast tumor cells are harvested by washing the monolayer with PBS, incubating cells in 0.05% trypsin and 0.53 mM EDTA (Gibco), and resuspending them in culture medium. The cells are washed twice with PBS containing 1% FBS and the pellet is incubated for 30 minutes on ice with 50 μl of 400 μM 7-aminoactinomycin D (7AAD) (Molecular Probes, Eugene, Oreg.), a vital dye which stains all permeable cells. Cells are then fixed with 1.0 ml of 0.5% paraformaldehyde in PBS and simultaneously permeabilized and stained for 16 hours at 4° C. with 220 μl of 10 μg/ml HOECHST 33342™ dye (also a DNA binding dye) containing 5% TWEEN 20™.

The data from 1×10⁴ cells are collected and stored using LYSYS II™ software and analyzed using PAINT-A-GATE™ software (Becton Dickinson). Darzynkiewica et al., Cytometry, 13:795-808 (1992); Picker et al., J. Immunol., 150:1105-1121 (1993). The viability and percentage of cells in each stage of the cell cycle are determined on gated single cells using 7AAD and Hoechst staining, respectively. (Cell doublets are excluded by pulse analysis of width vs. area of the Hoechst signal.) Cell numbers are determined using a hemocytometer.

4. DNA Synthesis ((³H)-Thymidine Incorporation Assay)

The assay was performed exactly as described in Example 12, except that the WISP polypeptides used as test proteins were replaced by the polyclonal antibodies generated in New Zealand White rabbits against murine WISP-1 and human WISP-2 described in Example 13, and not all the cell lines in Example 12 were tested. The results are shown in Table II: TABLE II ³H-Thymidine Incorporation Assay Results Cell line Type ATCC No. pAB.mWISP-1 pAB.mWISP-2 HT-29 adenocarcinoma HTB-38 No change No change (human moderately colon) well-differentiated Wi-Dr adenocarcinoma CCL-218 No change No change (human colon) N MuMG normal stimulates ˜3X (mouse mammary gland) NRK-49F normal fibroblast stimulates ˜2X (rat kidney) RAG adenocarcinoma stimulates ˜4.X (mouse kidney) NIH/3T3 fibroblast stimulates ˜2X (mouse embryo)

It is seen that the polyclonal antibodies to mouse WISP-1 and to human WISP-2 exhibited both stimulatory and inhibitory effects on proliferation of normal and tumor cells, depending on the cell line employed.

5. Affinity of Binding to Putative Receptor

Radioiodinated anti-WISP-1 and anti-WISP-2 antibodies are prepared by the IODOGEN™ method. Fracker et al., Biochem. Biophys. Res. Comm., 80:849-857 (1978). Binding assays are performed using appropriate receptor-expressing cells (such as, for mouse anti-WISP antibodies, MLG, a mouse lung cell line available from the ATCC) cultured in 96-well tissue culture plates (Falcon, Becton Dickinson Labware, Lincoln Park, N.J.). The cells are trypsinized and seeded in wells of 96-well plates at a density of 10⁴ cells/well and allowed to adhere overnight. The monolayers are washed with cold culture medium supplemented with 0.1% sodium azide and then incubated in triplicate with 100 μl of serial dilutions of ¹²⁵-anti-WISP-1 or WISP-2 antibodies in cold culture medium containing 0.1% sodium azide for 4 hours on ice. Non-specific binding is estimated by the preincubation of each sample with a 100-fold molar excess of nonradioactive antibodies in a total volume of 100 μl. Unbound radioactivity is removed by two washes with cold medium containing 0.1% sodium azide. The cell-associated radioactivity is detected in a gamma counter after solubilization of the cells with 150 μl of 0.1 M NaOH/well. The WISP-1 and WISP-2 binding constants (Kd) and anti-WISP antibody binding affinities are determined by Scatchard analysis.

It is expected that the antibodies against WISP-1 and WISP-2 will affect the growth of these cells.

Example 15 Further Uses of Antibodies that Bind WISP Polypeptide

1. WISP-1 and WISP-2

This example shows that the WISP-1 and WISP-2 genes are amplified in the genome of certain human lung, colon, and/or breast malignant tumors and/or cell lines. Amplification is associated with overexpression of the gene product, indicating that the WISP-1 and WISP-2 proteins are useful targets for therapeutic intervention in certain cancers such as colon, lung, breast, and other cancers. A therapeutic agent may take the form of antagonists of WISP molecules, for example, murine-human, chimeric, humanized, or human antibodies against WISP-1 and WISP-2, such as the antibodies prepared as described above.

The starting material for the screen was genomic DNA isolated from a variety of cancers. The DNA is quantitated precisely, e.g., fluorometrically. As a negative control, DNA was isolated from the cells of ten normal healthy individuals, pooled, and used as an assay control for the gene copy in healthy individuals.

The 5′ nuclease assay (for example, TAQMAN™) and real-time quantitative PCR (for example, ABI PRIZM 7700™ Sequence Detection System™ (Perkin Elmer, Applied Biosystems Division, Foster City, Calif.)), were used to find series potentially amplified in certain cancers. The results were used to determine whether the DNAs encoding WISP-1 and WISP-2 are over-represented in any of the primary lung or colon cancers or cancer cell lines or breast cancer cell lines that were screened. The primary lung cancers were obtained from indiviuals with tumors of the type and stage as indicated in Table III. An explanation of the abbreviations used for the designation of the primary tumors listed in Table III and the primary tumors and cell lines referred to throughout this example is given below:

Human lung carcinoma cell lines include A549 (SRCC768), Calu-1 (SRCC769), Calu-6 (SRCC770), H157 (SRCC771), H441 (SRCC772), H460 (SRCC773), SKMES-1 (SRCC774) and SW900 (SRCC775), all available from ATCC. Primary human lung tumor cells usually derive from adenocarcinomas, squamous cell carcinomas, large cell carcinomas, non-small cell carcinomas, small cell carcinomas, and broncho alveolar carcinomas, and include, for example, SRCC724 (squamous cell carcinoma abbreviated as “SqCCa”), SRCC725 (non-small cell carcinoma, abbreviated as “NSCCa”), SRCC726 (adenocarcinoma, abbreviated as “AdenoCa”), SRCC727 (adenocarcinoma), SRCC728 (squamous cell carcinoma), SRCC729 (adenocarcinoma), SRCC730 (adeno/squamous cell carcinoma), SRCC731 (adenocarcinoma), SRCC732 (squamous cell carcinoma), SRCC733 (adenocarcinoma), SRCC734 (adenocarcinoma), SRCC735 (broncho alveolar carcinoma, abbreviated as “BAC”), SRCC736 (squamous cell carcinoma), SRCC738 (squamous cell carcinoma), SRCC739 (squamous cell carcinoma), SRCC740 (squamous cell carcinoma), and SRCC740 (lung cell carcinoma, abbreviated as “LCCa”).

Colon cancer cell lines include, for example, ATCC cell lines SW480 (adenocarcinoma, SRCC776), SW620 (lymph node metastasis of colon adenocarcinoma, SRCC777), COL0320 (adenocarcinoma, SRCC778), HT29 (adenocarcinoma, SRCC779), HM7 (carcinoma, SRCC780), CaWiDr (adenocarcinoma, srcc781), HCT116 (carcinoma, SRCC782), SKC01 (adenocarcinoma, SRCC-83), SW403 (adenocarcinoma, SRCC784), LS174T (carcinoma, SRCC785), and HM7 (a high mucin producing variant of ATCC colon adenocarcinoma cell line LS 174T, obtained from Dr. Robert Warren, UCSF). Primary colon tumors include colon adenoocarcinomas designated CT2 (SRCC742), CT3 (SRCC743), CT8 (SRCC744), CT10 (SRCC-45), CT12 (SRCC746), CT14 (SRCC747), CT15 (SRCC748), CT17 (SRCC750), CT1 (SRCC751), CT4 (SRCC752), CT5 (SRCC753), CT6 (SRCC754), CT7 (SRCC755), CT9 (SRCC756), CT11 (SRCC757), CT18 (SRCC758), and DcR3, BACrev, BACfwd, T160, and T159.

Human breast carcinoma cell lines include, for example, HBL100 (SRCC759), MB435s (SRCC760), T47D (SRCC761), MB468 (SRCC762), MB175 (SRCC763), MB361 (SRCC764), BT20 (SRCC765), MCF7 (SRCC766), and SKBR3 (SRCC767).

The results are reported in delta (Δ) CT units. One unit corresponds to one PCR cycle or approximately a 2-fold amplification relative to normal, two units corresponds to 4-fold, 3 units to 8-fold amplification and so on. Quantitation was obtained using primers derived from the 3′-untranslated regions of the WISP-1 and WISP-2 cDNAs and a TAQMAN™ fluorescent probe corresponding to the respective intervening sequences. Using the 3′ region tends to avoid crossing intron-exon boundaries in the genomic DNA, an essential requirement for accurate assessment of gene amplification using this method. The sequences for the primers and probes (forward, reverse, and probe) used for the WISP-1-encoding and WISP-2-encoding gene amplification were as follows: WISP-1 Probe and primers: hu.WISP1.TMP (probe) (SEQ ID NO:138) 5′-AGCCTTTCCAAGTCACTAGAAGTCCT, GCTGG hu.WISP1.TMF (forward primer) (SEQ ID NO:139) 5′-CTGGACTACACCCAAGCCTGA hu.WISP1.TMR (reverse primer) (SEQ ID NO:140) 5′-CATTTCTTGGGATTTAGGCAAGA WISP-2 probe and primers: DNA33473.3utr-5 (forward primer) (SEQ ID NO:141) 5′-TCTAGCCCACTCCCTGCCT DNA33473.3utr-3 (reverse primer) (SEQ ID NO:142) 5′-GAAGTCGGAGAGAAAGCTCGC DNA33473.3utr-probe (SEQ ID NO:143) 5′-CACACACAGCCTATATCAAACAT′UCACACG

The 5′ nuclease assay reaction is a fluorescent PCR-based technique which makes use of the 5′ exonuclease activity of Taq DNA polymerase enzyme to monitor amplification in real time. Two oligonucleotide primers are used to generate an amplicon typical of a PCR reaction. A third oligonucleotide, or probe, is designed to detect nucleotide sequence located between the two PCR primers. The probe is non-extendible by Taq DNA polymerase enzyme, and is labeled with a reporter fluorescent dye and a quencher fluorescent dye. Any laser-induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together as they are on the probe. During the amplification reaction, the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner. The resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore. One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.

The 5′ nuclease procedure is run on a real-time quantitative PCR device such as the ABI PRIM 7700™ Sequence Detection System™. The system consists of a thermocyler, laser, charge-coupled device (CCD), camera and computer. The system amplifies samples in a 96-well format on a thermocycler. During amplification, laser-induced fluorescent signal is collected in real-time through fiber optics cables for all 96 wells, and detected at the CCD. The system includes software for running the instrument and for analyzing the data.

5′-Nuclease assay data are initially expressed as Ct, or the threshold cycle. This is defined as the cycle at which the reporter signal accumulates above the background level of fluorescence. The ΔCt values are used as quantitative measurement of the relative number of starting copies of a particular target sequence in a nucleic acid sample when comparing cancer DNA results to normal human DNA results.

The results of the first run performed are shown in FIGS. 19A-D and 20A-D for WISP-1 and WISP-2, respectively, and controls. Note the pattern shown in FIG. 19B (marked huWISP-1). The standard deviation for two samples of normal human DNA is shown in the column marked Nor Hu. This was used as a quality control tool. If the standard deviation was unacceptably large, the entire run was repeated. The nine additional columns corresponded to the human colon cancer cell lines noted above. The delta CT's for HT29 and WIDr were >3, corresponding to an about 8-fold over-representation of the WISP-1 gene in these samples compared to the normal samples. Similarly, FIG. 19B suggests an about 4-fold amplification of WISP-1 in the HCT116, SKCo-1, and SW403 cell lines.

As a comparison, see FIG. 20B (marked huFASr). The generally small delta CT values indicate that this gene was not significantly amplified in any of the cell lines (the value of 1 for SW620 corresponding to 2-fold amplification is within the noise level for the assay)

The WISP-1 result was confirmed in three replicate reactions. See FIGS. 21A-D, 22A-D, and 23A-C. The pattern and delta CT values obtained were very similar in FIGS. 21A-C (marked huWISP-1c, huWISP-1b, and huWISP-1a, respectively). The result was essentially identical to that obtained in the first run. HT29 and WIDr showed the highest levels of WISP-1 amplification, while HCT116, SKCo-1, and SW403 cell lines showed somewhat lower levels of WISP-1 gene amplification. Two additional reactions from a third run were confirmatory. See FIGS. 25A and 25B.

The WISP-1 gene is located on chromosome 8, in the general vicinity of the myc gene, which is known to be amplified in some colon cancer cell lines. The pattern obtained using primers and probe for the myc gene, namely, hu.c-myc.tm.p (SEQ ID NO:144) 5′-CTTGAGACTGAAAGATTTAGCCATAATGTAAACTGCCT hu.c-myc.tm.f (SEQ ID NO:145) 5′-CAAATGCAACCTCACAACCTTG, and hu.c-myc.tm.r (SEQ ID NO:146) 5′-TTCTTTTATGCCCAAAGTCCAATT, is consistent with a published report (Cancer Research, 57: 1769-1775 (1997)), tending to validate the 5′ nuclease assay method, but is clearly different from that obtained for WISP-1. These data prove that the myc gene is not the target of the amplification detected using the primers and probes for WISP-1.

The data using primers and probes based on the WISP-2 DNA sequence suggest that this gene may be the target of low-level gene amplification in most of the cell 14 nes examined. See FIGS. 20C, 22A-D, and 25C and D. Hence, antibodies to both WISP-1 and WISP-2, particularly humanized antibodies, are expected to be of benefit in combating certain types of cancer such as colon cancer, similar to the humanized anti-HER-2 antibody in clinical use.

2. WISP-2

Description of Tumors and Cell Lines

Amplification using several different tumor types was performed for human WISP-2 (PR0261), as described below. Table III describes the stage, T stage, and N stage of various primary tumors which were used to screen the WISP-2 compound of the invention. TABLE III Primary Lung and Colon Tumor Profiles Other Dukes T N Primary Tumor Stage Stage Stage Stage Stage Human lung tumor SqCCA (SRCC724) IB — — T1 N1 [LT1] Human lung tumor NSCCa (SRCC725) IA — — T3 NO [LT1a] Human lung tumor AdenoCa (SRCC726) IB — — T2 NO (LT2) Human lung tumor AdenoCa (SRCC727) IB — — T1 N2 (LT3) Human lung tumor SqCCq (SRCC728) IIB — — T2 NO [LT4] Human lung tumor AdenoCa (SRCC729) IV — — T1 NO [LT6] Human lung tumor Aden/SqCCa IB — — T1 NO (SRCC730) [LT7] Human lung tumor AdenoCa (SRCC731) IIB — — T2 NO [LT9] Human lung tumor SqCCa (SRCC732) IA — — T2 N1 [LT10] Human lung tumor AdenoCa (SRCC733) IB — — T1 N1 [LT11] Human lung tumor AdenoCa (SRCC734) IIA — — T2 NO [LT12] Human lung tumor BAC (SRCC735) IB — — T2 NO [LT13] Human lung tumor SqCCa (SRCC736) IB — — T2 NO [LT15] Human lung tumor SqCCa (SRCC737) IB — — T2 NO [LT16] Human lung tumor SqCCa (SRCC738) IIB — — T2 N1 [LT17) Human lung tumor SqCCa (SRCC739) IB — — T2 NO [LT18] Human lung tumor SqCCa (SRCC740) IB — — T2 NO [LT19] Human lung tumor LCCa (SRCC741) IIB — — T3 N1 [LT21] Human colon AdenoCa (SRCC742) (CT2] — M1 D pT4 NO Human colon AdenoCa (SRCC743) [CT3] — B pT3 NO Human colon AdenoCa (SRCC 744) [CT8] B T3 NO Human colon AdenoCa (SRCC745) A pT2 NO [CT10] Human colon AdenoCa (SRCC746) MO, R1 B T3 NO [CT12] Human colon AdenoCa (SRCC747) pMO, RO B pT3 pNO [CT14] Human colon AdenoCa (,(;RCC748) M1, R2 D T4 N2 (CT15] Human colon AdenoCa (SRCC749) pMO B pT3 pNO [CT16] Human colon AdenoCa (SRCC750) C1 pT3 pN1 [CT17] Human colon AdenoCa (SRCC751) [CT1] MO, R1 B pT3 NO Human colon AdenoCa (SRCC752) (CT4] B pT3 MO Human colon AdenoCa (SRCC753) (CT5] G2 C1 pT3 pNO Human colon AdenoCa (SRCC754) [CT6] PMO, RO B pT3 pNO Human colon AdenoCa (SRCC755) [CT7] G1 A pT2 pNO Human colon AdenoCa (SRCC756) [CT9] G3 D pT4 pN2 Human colon AdenoCa (SRCC757) B T3 NO [CT11] Human colon AdenoCa (SRCC758) MO, RO B pT3 pNO [CT18]

DNA Preparation:

DNA was prepared from cultured cell lines, primary tumors, and normal human blood (controls and framework and epicenter mapping). The isolation was performed using purification kit #13362 (which includes 10 purification tips with a capacity of 400 μg genomic DNA each), buffer set #1960 and protease #19155 and #19101, all from Quiagen, according to the manufacturer's instructions and the description below.

Cell Culture Lysis:

Cells were washed and trypsinized at a concentration of 7.5×10⁸ per tip and pelleted by centrifuging at 1000 rpm for 5 minutes at 4° C., followed by washing again with 112 volume of PBS recentrifugation. The pellets were washed a third time, and the suspended cells collected and washed 2× with PBS. The cells were then suspended into 10 mL PBS. Buffer C1 was equilibrated at 4° C. Protease #19155 (Quiagen) was diluted into 6.25 ml cold ddH₂O to a final concentration of 20 mg/ml and equilibrated at 4° C. 10 mL of G2 Buffer was prepared by diluting RNAse A stock (Quiagen) (100 mg/ml) to a final concentration of 200 μg/ml.

Buffer C1 (10 mL, 4° C.) and ddH2O (40 mL, 4° C.) were then added to the 10 mL of cell suspension, mixed by inverting and incubated on ice for 10 minutes. The cell nuclei were pelleted by centrifuging in a BECKMAN™ swinging bucket rotor at 2500 rpm at 4° C. for 15 minutes. The supernatant was discarded and the nuclei were suspended with a vortex into 2 mL Buffer C1 (at 4° C.) and 6 mL ddH₂O, followed by a second 4° C. centrifugation at 2500 rpm for 15 minutes. The nuclei were then resuspended into the residual buffer using 200 μl per tip. G2 buffer (10 ml) was added to the suspended nuclei while gentle vortexing was applied. Upon completion of buffer addition, vigorous vortexing was applied for 30 seconds. Quiagen protease (200 pl, prepared as indicated above) was added and incubated at 50° C. for 60 minutes. The incubation and centrifugation were repeated until the lysates were clear (e.g., incubating an additional 30-60 minutes, pelleting at 3000×g for 10 min., 4° C.).

Solid Human Tumor Sample Preparation and Lysis:

Tumor samples were weighed and placed into 50-ml conical tubes and held on ice. Processing was limited to no more than 250 mg tissue per preparation (1 tip/preparation). The protease solution was freshly prepared by diluting into 6.25 ml cold ddH₂O to a final concentration of 20 mg/ml and stored at 4° C. G2 buffer (20 ml) was prepared by diluting DNAse A to a final concentration of 200 mg/ml (from 100 mg/ml stock). The tumor tissue was homogenated in 19 ml G2 buffer for 60 seconds using the large tip of the polytron in a laminar-flow TC hood to order to avoid inhalation of aerosols, and held at room temperature. Between samples, the polytron was cleaned by spinning at 2×30 seconds each in 2L ddH₂O, followed by G2 buffer (50 ml) If tissue was still present on the generator tip, the apparatus was disassembled and cleaned.

Protease (Quiagen), prepared as indicated above, 1.0 ml, was added, followed by vortexing and incubation at 50° C. for 3 hours. The incubation and centrifugation were repeated until the lysates were clear (e.g., incubating additional 30-60 minutes, pelleting at 3000×g for 10 min., 4° C.).

Human Blood Preparation and Lysis:

Blood was drawn from healthy volunteers using standard infectious agent protocols and citrated into 10 ml samples per tip. Protease (Quiagen) was freshly prepared by dilution into 6.25 ml cold ddH₂O to a final concentration of 20 mg/ml and stored at 4° C. G2 buffer was prepared by diluting RNAse A to a final concentration of 200 μg/ml from 100 mg/ml stock. The blood (10 ml) was placed into a 50-ml conical tube, and 10 ml C1 buffer and 30 ml ddH₂O (both previously equilibrated to 4° C.) were added, and the components mixed by inverting and held on ice for 10 minutes. The nuclei were pelleted with a BECKMAN™ swinging bucket rotor at 2500 rpm, 4° C. for 15 minutes and the supernatant was discarded. With a vortex, the nuclei were suspended into 2 ml C1 buffer (4° C.) and 6 ml ddH₂O (4° C.). Vortexing was repeated until the pellet was white. The nuclei were then suspended into the residual buffer Using a 200-μl tip. G2 buffer (10 ml) was added to the suspended nuclei while gently vortexing, followed by vigorous vortexing for 30 seconds. Protease (Quiagen) was added (200 pl) and incubated at 50° C. for 60 minutes. The incubation and centrifugation were repeated until the lysates were clear (e.g., incubating an additional 30-60 minutes, pelleting at 3000×g for 10 min., 4° C.).

Purification of Cleared Lysates; Isolation of Genomic DNA:

Genomic DNA was equilibrated (1 sample per maxi tip preparation) with 10 ml QBT buffer. QF elution buffer was equilibrated at 50° C. The samples were vortexed for 30 seconds, then loaded onto equilibrated tips and drained by gravity. The tips were washed with 2×15 ml QC buffer. The DNA was eluted into 30-ml silanized, autoclaved 30-ml COREX™ tubes with 15-ml QF buffer (50° C.). Isopropanol (10.5 ml) was added to each sample, and the tubes were covered with paraffin and mixed by repeat ed inversion until the DNA precipitated. Samples were pelleted by centrifugation in the SS-34 rotor at 15,000 rpm for 10 minutes at 4° C. The pellet location was marked, the supernatant discarded, and 10 ml 70% ethanol (4° C.) was added. Samples were pelleted again by centrifugation on the SS-34 rotor at 10,000 rpm for 10 minutes at 4° C. The pellet location was marked and the supernatant discarded. The tubes were then placed on their side in a drying rack and dried 10 minutes at 37° C., taking care not to overdry the samples.

After drying, the pellets were dissolved into 1.0 ml TE (pH 8.5) and placed at 50° C. for 1-2 hours. Samples were held overnight at 4° C. as dissolution continued. The DNA solution was then transferred to 1.5-ml tubes with a 26-gauge needle on a tuberculin syringe. The transfer was repeated 5× in order to shear the DNA. Samples were then placed at 50° C. for 1-2 hours.

Quantitation of Genomic DNA and Preparation for Gene Amplification Assay:

The DNA levels in each tube were quantified by standard A260, A280 spectrophotometry on a 1:20 dilution (5 μl DNA+95 pl ddH₂O) using the 0.1-ml quartz cuvettes in the BECKMAN DU640™ spectrophotometer. A260/A280 ratios were in the range of 1.8-1.9. Each DNA sample was then diluted further to approximately 200 ng/ml in TE (pH 8.5). If the original material was highly concentrated (about 700 ng/μl), the material was placed at 50° C. for several hours until resuspended.

Fluorometric DNA quantitation was then performed on the diluted material (20-600 ng/ml) using the manufacturer's guidelines as modified below. This was accomplished by allowing a HOEFFER DYNA QUANT 200™ fluorometer to warm up for about 15 minutes. The HOECHST™ dye working solution (#H33258, 10 μl, prepared within 12 hours of use) was diluted into 100 ml 1×TNE buffer. A 2-ml cuvette was filled with the fluorometer solution, placed into the machine, and the machine was zeroed. pGEM 3Zf(+) (2 μl, lot #360851026) was added to 2 ml of fluorometer solution and calibrated at 200 units. A second 2 μl of pGEM 3Zf(+) DNA was then tested and the reading confirmed at 400+/−10 units. Each sample was then read at least in triplicate. When 3 samples were found to be within 10% of each other, their average was taken and this value was used as the quantification value.

The fluorometrically-determined concentration was then used to dilute each sample to 10 ng/μl in ddH₂O. This was done simultaneously on all template samples for a single TAQMAN™ plate assay, and with enough material to run 500-1000 assays. The samples were tested in triplicate with both B-actin and GAPDH on a single plate with normal human DNA and no-template controls. The diluted samples were used, provided that the CT value of normal human DNA subtracted from test DNA was +/−1 CT. The diluted, lot-qualified genomic DNA was stored in 1.0-ml aliquots at −80° C. Aliquots which were subsequently to be used in the gene amplification assay were stored at 4° C. Each 1-ml aliquot is enough for 8-9 plates or 64 tests.

Framework Mapping and Epicenter Marking:

Human WISP-1 was reexamined with both framework and epicenter mapping. Selected tumors from the above initial screen were reexamined with both framework and epicenter mapping. Table IV indicates the chromosomal mapping of the framework markers that were used in the present example. The framework markers are located approximately every 20 megabases along Chromosome 8 and were used to control for aneuploidy. TABLE IV Framework Markers Map Position on Stanford Human Genome Chromosome 8 Center Marker Name H9 EST-00040 H59 WI-961 H121 SHGC-11323 H200 SHGC-7433 H256 AFMa183zfl

Table V describes the epicenter markers that were employed in association with WISP-1. These markers are located in close proximity to the gene for WISP-1 and are used to assess the amplification status of the region of chromosome 8 in which the gene for WISP-1 is located. The distance between individual markers is measured in centirays (cR), which is a radiation. breakage unit approximately equal to a 1% chance of a breakage between two markers. One cR is very roughly equivalent to 20 kilobases. The marker SHGC-32958 is the marker found to be the closest to the location on chromosome 8 to which the gene encoding WISP-1 most closely maps. TABLE V Epicenter Markers Map Position on Stanford Human Genome Distance to next Chromosome 8 Center Marker Name Marker (cR) H257 AFMa248te1 103(gap) H259 SHGC-36664 33 H261 AFM259xc5 63 H266 SHGC-32958 41 H267 AFMa175xc1 19 H268 AFM337wg5 87 H273 SHGC-33759 71 H274 SHGC-32752  5 H275 WI-7711 21 H277 HGC-34940 —

The framework markers for human WISP-2 are located approximately every 20 megabases along Chromosome 20, and are used to control for aneuploidy. The markers are shown in Table VI. TABLE VI Framework Markers Map Position on Stanford Human Genome Chromosome 20 Center Marker Name T10 SHGC-2797 T48 UT759 T73 AFMa339xf5 T115 SHGC-33922 T159 HGC-36268

The marker SHGC-33922 is the marker to which human WISP-2 DNA most closely maps. This marker is between the framework markers.

Framework analysis showed that all markers were up in tumors; thus, chromosome 20 was aneuploid in many, tumors. Since the markers were up due to aneuploidy, epicenter analysis was not done for human WISP-2 gene.

The ΔCt values of the above described framework markers along Chromosome 8 relative for WISP-1 are indicated for selected tumors in Tables VII and VIII. TABLE VII Amplification of framework markers relative to Human WISP-1 DNA Framework Markers (Δct) Probe/Delta CT C-myc WISP-1 WISP-2 H9 H59 H121 H200 H256 Template (SD) (SD) (SD) (SD) (SD) (SD) (SD) (SD) Nor Hu 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 (0.91) (0.01) (0.20) (0.13) (0.20) (0.14) (0.16) (0.04) SW480 1.86 0.84 1.92 −1.18 1.01 0.17 0.165 0.81 SW620 1.45 0.98 1.60 0.45 0.75 1.00 0.81 0.52 Colo320 3.73 0.65 1.88 0.69 0.70 0.89 0.60 0.40 HT29 0.83 2.67 2.20 −1.13 −0.40 −0.55 1.00 2.42 HM7 −2.03 0.07 −0.28 −0.28 0.24 −0.48 0.12 −0.26 WiDr −0.13 2.91 1.67 −0.20 0.95 0.0′7 1.43 2.55 HCT116 −0.57 1.82 1.04 1.24 1.56 0.84 1.76 1.53 SKCO-1 0.19 1.68 0.97 −0.30 0.32 0.12 1.39 1.63 SW403 −0.72 1.34 1.77 0.23 0.53 0.26 1.48 1.48 Nor Hu — 0.00 0.00 0.00 0.00 0.00 0.00 0.00 (0.18) (1.02) (0.08) (0.13) (0.01) (0.16) (0.37) CT-2 — 0.65 0.44 −0.25 0.11 0.07 0.13 0.95 CT-3 — 0.90 0.95 −0.27 0.05 −0.10 −0.11 0.32 CT-8 — 0.47 −0.34 0.07 −0.20 0.00 −0.04 0.07 CT-10 — 0.76 0.50 0.23 −0.36 −0.08 0.17 0.70 CT-12 — 1.30 2.14 −0.70 −0.45 0.24 0.47 1.75 CT-14 — 1.17 −0.48 0.05 0.18 0.31 0.23 1.5! CT-15 — 0.22 −0.13 0.13 −0.48 0.29 0.11 0.59 CT-16 — 0.26 0.10 0.00 −0.15 −0.23 −0.09 0.95 CT-17 — 0.57 −0.33 0.73 −0.11 −0.05 −0.11 0.25 Nor Hu — 0.00 0.00 0.00 0.00 0.00 0.00 0.00 (0.45) (1.07) (0.04) (0.21) (0.18) (0.03) (0.18) CT-1 — 0.64 −0.37 −0.36 0.19 0.68 0.01 0.66 CT-4 — 0.15 −0.23 −1.00 0.24 −0.11 0.30 0.14 CT-5 — 0.86 −1.23 −0.60 −0.25 0.22 0.51 0.62 CT-6 — 0.03 0.39 −0.24 0.61 0.70 0.01 0.19 CT-7 — −0.20 −1.36 −0.76 0.00 −0.09 −0.13 −0.16 CT-9 — 0.30 −0.54 −0.50 0.29 0.54 0.11 0.18 CT-11 — 0.48 0.14 −0.89 0.34 0.82 0.17 −0.06 CT-18 — −0.20 −1.37- −0.52 0.32 0.66 0.08 0.12

TABLE VIII Amplification of framework markers relative to Human WISP-1 DNA Framework Markers (8ct) Probe/Delta CT Template WISP-2 (SD) T10 (SD) T48 (SD) T73 (SD) T115 (SD) T159 (SD) Nor Hu 0.00 0.00 0.00 0.00 0.00 0.00 (0.05) (0.16) (0.09) (0.21) (3.22) (0.09) SW480 1.31 1.32 0.63 1.94 −5.66 1.61. SW620 1.32 2.02 1.42 1.06 −10.95 1.48 Colo320 0.43 1.35 1.37 0.61 0.30 1.37 HT29 1.76 1.09 −2.23 1.26 −5.47 1.87 HM7 −0.32 0.32 0.38 0.41 −6.3 0.48 WiDr 1.76 1.61 −1.38 1.04 −7.36 1.55 HCT116 1.18 1.24 1.15 1.46 −8.38 1.49 SKCO-1 1.40 1.17 1.19 1.13 −5.34 1.61 SW403 1.92 2.24 −17.23 1.38 −3.66 2.12

Gene Amplification Assay Results:

The human WISP-2 (PR0261) compound of the invention was screened in the following primary tumors and the resulting ΔCt values are reported in Table IX. TABLE IX ΔCt values in lung and colon primary tumor models Primary Tumor PR0261 LT1 0.41 LT1a 1.08 LT2 0.27 LT3 0.98 LT4 0.32 LT6 0.45 LT7 0.03 LT9 0.18 LT10 1.16 LT11 0.67, 1.59, 0.63, 0.19, LT12 0.80, 1.73, 1.08, 2.23 LT13 1.02, 1.13, 1.01, 0.29 LT15 0.97, 2.64, 0.56, 2.38 LT16 0.80, 0.75, 0.82, 2.05 LT17 1.67, 2.01, 1.43, 0.93 LT18 1.22, 0.46, 0.15, −0.17 LT19 0.76, 1.38, 1.39, 2.33 LT21 0.04, 1.14, 0.48, 3.40 CT2 1.66 CT3 2.14 CT8 0.55 CT10 1.00 CT12 0.34 CT14 1.03 CT15 0.67 CT16 0.87 CT17 −0.19 M −0.06 CT4 1.00 CT5 1.07 CT6 −0.08 CT7 0.15 CT9 0.68 CT11 0.59 CT18 0.73 A549 — Calu-1 Calu-6 H157 H441 H460 SKMES1 SW900 — SW480 0.62, 1.86, 1.90, 1.91, 1.20, 2.36, 1.57, 1.68, 1.68, 1.53, 1.36, 2.50 1.59, SW620 0.66, 1.98, 1.65, 1.57, 1.85, 1.83, 1.63, 1.41, 1.61, 1.42, 1.24, 1.59 1.52, Colo320 −0.33, 2.49, 0.66, 0.99, 0.48, 1.06, 0.91, 1.24, 0.72, 1.04, 0.33, 0.46, 0.2-- HT29 0.46, 2.00, 1.95, 2.59, 1.61, 2.59, 2.58, 1.39, 1.49, 1.32 1.38, 1.40, HM7 −0.70, 0.54, 0.74, 0.67, −0.29, 0.66, 0.27, 0.-08, 0.64, 0.34, 0.09, 0.29, 0.21 WiDr 0.19, 1.84, 1.64, 1.58, 1.00, 0.91, 1.71, 0.87 1.44, 1.57, 0.93, HCT116 0.25, 1.08, 1.29, 2.05, 1.04, 1.81, 2.01, 1.56, 1.29, 1.05, 1.07, 1.09, 0.96 SKC01 0.73, 2.10, 1.99, 1.50, 1.33, 2.13, 1.00, 1.33, 1.33, 1.29 1.26, 1.19 SW403 0.26, 2.15, 1.98, 1.52, 1.42, 1.67, 2.20, 2.19, 2.40, 1.40, 1.50, 1.291.43, LS174T 1.48 HBL100 1.40 MB435s 1.43 T47D 0.38 MB468 −0.08 MB175 0.23 MB361 0.37 BT20 1.66 MCF7 0.53 SKBR3 1.73

The ΔCt values for DNA33473 (PR0261; human WISP-2) in a variety of primary lung and colon tumors as well as lung tumor cell lines are reported in Table IX. A ΔCt value of >1 was typically used as the threshold value for amplification scoring, as this represents a doubling of the gene copy. Table IX indicates that significant amplification of DNA33474 occurred in: primary lung tumors LT1a, LT10, LT12, LT15, LT17 and LT19; (2) primary colon tumors CT2, CT3, CT14, and CT5; (3) colon tumor cell lines SW480, SW620, HT29, WiDr, HCT116, SKC01, SW403, and LS174T and (4) breast tumor cell lines HBL100, MB435s, BT20 and SKBR3.

The ΔCt and average ΔCt values for the primary lung tumors were the following: 1.08, 1.16, 1.17, 1.64, 1.50 and 1.47, respectively; those for the primary colon tumors were 1.16, 2.14, 1.03 and 1.07, respectively; those for the colon tumor cell lines were 1.67, 1.54, 1.73, 1.24, 1.32, 1.35, 1.65, and 1.48, respectively; and those for the breast tumor cell lines were 1.40, 1.43, 1.66, and 1.73, respectively.

For the lung tumors, this represents approximately a 2.1-, 2.2-, 2.2-, 3.1-, 2.8-, and 2.8-, respectively, fold increase in gene copy relative to normal tissue. For the colon tumors, this represents a 2.2-, 4.4-, 2.0-, and 2.1-, respectively, fold increase in gene copy relative to normal tissue. For the colon tumor cell lines, this represents a 3.2-, 2.9-, 3.3-, 2.4-, 2.5-, 2.5-, 3.1-, and 2.8-, respectively, fold increase in gene copy relative to normal tissue. For the breast tumor cell lines, this represents a 2.6-, 2.7-, 3.2-, and 3.3-, respectively, fold increase in gene copy relative to normal tissue. Because amplification of DNA33473 (PR0261) occurs in various tumors, it is likely associated with tumor formation or growth. As a result, antagonists (e.g., antibodies) directed against the protein encoded by DNA33473 (PR0261) would be expected to be useful in cancer therapy.

Example 16 In Situ Hybridization

In situ hybridization is a powerful and versatile technique for the detection and localization of nucleic acid sequences within cell or tissue preparations. It may be useful, for example, in identifying sites of gene expression, analyzing the tissue distribution of transcription, identifying and localizing viral infection, following changes in specific mRNA synthesis, and aiding in chromosome mapping.

In situ hybridization was performed following an optimized version of the protocol by Lu and Gillett, Cell Vision 1: 169-176 (1994), using PCR-generated ³³P-labeled riboprobes. Briefly, formalin-fixed, paraffin-embedded human tissues were sectioned, deparaffinized, deproteinated in proteinase K (20 g/ml) for 15 minutes at 37° C., and further processed for in situ hybridization as described by Lu and Gillett, supra. A (³³-P) UTP-labeled antisense riboprobe was generated from a PCR product and hybridized at 55° C. overnight. The slides were dipped in KODAK NTB2™ nuclear track emulsion and exposed for 4 weeks.

³³P-Riboprobe synthesis

6.0 μl (125 mCi) of ³³P-UTP (Amersham BF 1002, SA<2000 Ci/mmol) were speed-vacuum dried. To each tube containing dried ³³P-UTP, the following ingredients were added:

2.0 μl 5× transcription buffer

1.0 μl DTT (100 mM)

2.0 μl NTP mix (2.5 mM: 10 μl each of 10 mM GTP, CTP & ATP+10 μl H₂O)

1.0 μl UTP (50 μM)

1.0 μl RNAsin

1.0 μl DNA template (1 μg)

1.0 μl H₂

1.0 μl RNA polymerase (for PCR products T3=AS, T7=S, usually)

The tubes were incubated at 37° C. for one hour. A total of 1.0 μl RQ1 DNase was added, followed by incubation at 37° C. for 15 minutes. A total of 90 μl TE (10 mM Tris pH 7.6/1 mM EDTA, pH 8.0) was added, and the mixture was pipetted onto DE81 paper. The remaining solution was loaded in a MICROCON-50™ ultrafiltration unit, and spun using program 10 (6 minutes). The filtration unit was inverted over a second tube and spun using program 2 (3 minutes). After the final recovery spin, a total of 100 μl TE was added. Then 1 μl of the final product was pipetted on DE81 paper and counted in 6 ml of BIOFLUOR II™.

The probe was run on a TBE/urea gel. A total of 1-3 μl of the probe or 5 μl of RNA Mrk III was added to 3 μl of loading buffer. After heating on a 95° C. heat block for three minutes, the gel was immediately placed on ice. The wells of gel were flushed, and the sample was loaded and run at 180-250 volts for 45 minutes. The gel was wrapped in plastic wrap (SARAN™ brand) and exposed to XAR film with an intensifying screen in a −70° C. freezer one hour to overnight.

³³P-Hybridization

A. Pretreatment of Frozen Sections

The slides were removed from the freezer, placed on aluminum trays, and thawed at room temperature for 5 minutes. The trays were placed in a 55° C. incubator for five minutes to reduce condensation. The slides were fixed for 10 minutes in 4% paraformaldehyde on ice in the fume hood, and washed in 0.5×SSC for 5 minutes, at room temperature (25 ml 20×SSC+975 ml s.c. H₂O). After deproteination in 0.5 μg/ml proteinase K for 10 minutes at 37° C. (12.5 μl of 10 mg/ml stock in 250 ml prewarmed RNAse-free RNAse buffer), the sections were washed in 0.5×SSC for 10 minutes at room temperature. The sections were dehydrated in 70%, 95%, and 100% ethanol, 2 minutes each.

B. Pretreatment of Paraffin-Embedded Sections

The slides were deparaffinized, placed in s.c. H₂O, and rinsed twice in 2×SSC at room temperature, for 5 minutes each time. The sections were deproteinated in 20 μg/ml proteinase K (500 μl of 10 mg/ml in 250 ml RNAse-free RNAse buffer; 37° C., 15 minutes) for human embryo tissue, or 8× proteinase K (100 μl in 250 ml RNAse buffer, 37° C., 30 minutes) for formalin tissues. Subsequent rinsing in 0.5×SSC and dehydration were performed as described above.

C. Prehybridization

The slides were laid out in a plastic box lined with Box buffer (4×SSC, 50% formamide) The filter paper was saturated. The tissue was covered with 50 μl of hybridization buffer (3.75 g dextran sulfate+6 ml s.c. H₂O), vortexed, and heated in the microwave for 2 minutes with the cap loosened. After cooling on ice, 18.75 ml formamide, 3.75 ml 20×SSC, and 9 ml s.c. H₂O were added, and the tissue was vortexed well and incubated at 42° C. for 1-4 hours.

D. Hybridization

1.0×10⁶ cpm probe and 1.0 μl tRNA (50 mg/ml stock) per slide were heated at 95° C. for 3 minutes. The slides were cooled on ice, and 48 μl hybridization buffer was added per slide. After vortexing, 50 μl ³³P mix was added to 50 μl prehybridization on the slide. The slides were incubated overnight at 55° C.

E. Washes

Washing was done for 2×10 minutes with 2×SSC, EDTA at room temperature (400 ml 20×SSC+16 ml 0.25 M EDTA, V_(f)=4 L), followed by RNAseA treatment at 37° C. for 30 minutes (500 μl of 10 mg/ml in 250 ml RNAse buffer=20 μg/ml). The slides were washed 2×10 minutes with 2×SSC, EDTA at room temperature. The stringency wash conditions were as follows: 2 hours at 55° C., 0.1×SSC, EDTA (20 ml 20×SSC+16 ml EDTA, V_(f)=4 L).

F. Oligonucleotides

In situ analysis was performed on DNA sequences disclosed herein. The oligonucleotides employed for these analyses are as follows. (1) Mouse WISP-1 (Clone 568) Notrim-p1: (SEQ ID NO:147) 5′-GGA TTC TAA TAC GAC TCA CTA TAG GGC GTC CCT GGC CAG TGC TGT GAG-3′ Notrim-p2: (SEQ ID NO:148) 5′-CTA TGA AAT TAA CCC TCA CTA AAG GGA GGG CCA GGC TTT GCT TCC ATT-3′ (2) Human WISP-1 hmWISP-1 p1: (SEQ ID NO:149) 5′-GGA TTC TAA TAC GAC TCA CTA TAG GGC TGG AGG CAT GGC ACA GGA AC-31 hmWISP-1 p2: (SEQ ID NO:150) 5′-CTA TGA AAT TAA CCC TCA CTA AAG GGA TCC GGA TCA GGC TTG GGT GTA-3′ (3) Mouse WISP-2 (Clone 1367.3) 1367.p1: (SEQ ID NO:151) 5′-GGA TTC TAA TAC GAC TCA CTA TAG GGC AGC TTG GGA TGG AGG TCT TTC-3′ 1367.p2: (SEQ ID NO:152) 5′-CTA TGA AAT TAA CCC TCA CTA AAG GGA GGG CAC TGG GGT GGT GT-3′ (4) Human WISP-2 (DNA33473) DNA33473-p1: (SEQ ID NO:153) 5′-GGA TTC TAA TAC GAC TCA CTA TAG GGC GCG AGG ACG GCG GCT TCA-3′ DNA33473-p2: (SEQ ID NO:154) 5′-CTA TGA AAT TAA CCC TCA CTA AAG GGA AGA GTC GCG GCC GCC CTT TTT-3′ (5) Human WISP-3 WISP3-p1 (SEQ ID NO:155) 5′-GGA TTC TAA TAC GAC TCA CTA TAG GGC GGG GCT CCT CTT CTC CAC TCT-3′ WISP3-p2 (SEQ ID NO:156) 5′-CTA TGA AAT TAA CCC TCA CTA AAG GGA GCT GTC GCA AGG CTG AAT GTA-3′

G. Results

In situ analysis was performed on the above DNA sequences disclosed herein. The results from these analyses are as follows.

(1) Mouse WISP-1

Expression in Mouse Tissues

Mouse Fetal Tissues: In situ hybridization of mouse WISP-1 showed strong expression in embryonic mesenchymal tissues. At E10.5 expression was observed in tissues that would develop into skeletal elements in the adult; this pattern was maintained at later stages of embryonic development. In later stages (E12.5 and E15.5), expression was highest in osteoblasts at the sites of bone formation. Expression was also observed in the embryonic heart, where the signal was particularly strong in the atria at E12.5 (atria were not included in sections at E15.5).

Mouse Adult Tissues: No expression was observed in any of the adult tissues examined, including heart, lung, kidney, adrenal, liver, pancreas, cerebrum, and cerebellum. These results do not correlate with the Northern data.

Additional sites of expression in the fetus were the walls of developing blood vessels and in fibroblast-like cells within the hepatic portal tract mesenchyme.

Expression in Normal and Wnt-1 Transgenic Tumors

Expression with the antisense probe was observed over fibroblast-like cells lying adjacent to the subcutaneous skeletal muscle in P10 (post-natal day 10 pups) and in pregnant females. Expression was not observed over breast epithelial cells at any of the time points examined in the study.

Expression of mouse WISP-1 was high in all three of the Wnt-1 transgenic tumors tested and appeared to be confined to the supporting fibroblast-like cells within the delicate connective tissue stroma. Some expression was seen over the tumor cells themselves; however, this likely represents overspill from tumor fibroblasts, rather than true expression by tumor cells.

In summary, mouse WISP-1 was expressed in embryonic skeletal mesenchyme and at sites of bone formation. It was additionally expressed in fibroblasts in the sub-cutus of growing pups and pregnant females. It is likely to play a role in osteogenesis, and may be involved in repair after injury. Expression was also observed in the embryonic heart.

(2) Human WISP-1

Expression in Human Tissues

Human Fetal Tissue The fetal tissues examined (E12-E16 weeks) included: placenta, umbilical cord, liver, kidney, adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis, and lower limb.

Human WISP-1 exhibited expression at sites of connective tissue interfaces in the fetus, for example, developing portal tracts, fascial planes in muscle, and connective tissue surrounding developing skeletal elements and tendons. Expression also was seen in the epithelium of the developing renal cortex and in spindle-shaped fibroblast-like cells in the fetal adrenal. Human WISP-1 was strongly expressed by osteoblasts at sites of bone formation in the fetal limb.

Human Adult Tissue The adult tissues examined were: liver, kidney, adrenal, myocardium, aorta, spleen, lung, skin, chondrosarcoma, eye, stomach, gastric carcinoma, colon, colonic carcinoma, renal cell carcinoma, prostate, bladder mucosa, and gall bladder, as well as tissue with acetominophen-induced liver injury and hepatic cirrhosis.

No expression was seen in normal or diseased adult tissues in this study.

In summary, the overall pattern of expression of human WISP-1 was broadly similar to that observed for the mouse gene as noted above. The human WISP-1 probe did not cross react with the mouse embryo section.

Expression in Human Breast Carcinoma and Normal Breast Tissue

Human WISP-1 was negative on benign and malignant epithelial cells, but showed specific hybridization in mesenchmal cells, particularly in areas of tissue repair, including dystrophic ossification. Most positive cells had the morphology of fibroblasts; smooth muscle cells appeared to be negative.

In summary, this study shows expression of human WISP-1 RNA in mesenchymal cells involved in tissue repair and/or collagen deposition. The signal was particularly strong in benign fibroblast-like cells adjacent to either infiltrating breast carcinoma cells or tissue destruction due to benign, inflammatory conditions (duct rupture). Of note is the fact that deposition of benign osteoid seemed to correlate with strong expression of the RNA.

(3) Mouse WISP-2

Expression in Normal Mouse Tissues

Mouse Fetal Tissues: Expression of mouse WISP-2 was observed in osteoblasts in an E15.5 mouse embryo, within the developing mandible.

Mouse Adult Tissues: Expression of mouse WISP-2 was observed in stromal cells around the origin, and within the cusps of the mitral and tricuspid valves of the adult heart. Expression was also observed in the adventitial cells of the renal artery; expression was presumed to be present at this site in all arteries.

All other tissues were negative.

Expression in Wnt-1 Tumors

The results demonstrated specific expression of mouse WISP-2 in the stroma of all Wnt-1 tumors examined. There was a signal over mononuclear cells with open vesicular nuclei, possibly macrophages. No expression was observed in either the benign or the malignant epithelium.

(4) Human WISP-2

Expression in Human Tissues

Strong expression of the WISP-2-encoding gene was observed in dermal fibroblasts in normal adult skin. Additionally, strong expression was seen in two cirrhotic livers, at sites of active hepatic fibrosis. Moderate expression was found over fasiculata cells of adrenal cortex. This localization supports a role for human WISP-2 in extracellular matrix formation or turnover.

Expression in Human Breast Carcinoma and Normal Breast Tissue, and in Lung Carcinoma

Human WISP-2 showed a similar hybridization pattern to human WISP-1 (described above) in the two breast tumors examined. It was negative on benign and malignant epithelial cells, but showed specific hybridization in mesenchmal cells, particularly in areas of tissue repair, including dystrophic ossification. The signal appeared to localize to the same cell population for both probes WISP-1 and WISP-2; however, in some areas (breast tumor 02), the signal for WISP-2 was significantly stronger than that for human WISP-1. Most positive cells had the morphology of fibroblasts; smooth muscle cells appeared to be negative. The signal for human WISP-2 was less intense in the lung tumor tissue; however, this section also showed less tissue repair compared with the breast tumor slides. Normal lung and kidney tissue were essentially negative for human WISP-2, as for human WISP-1.

In summary, this study shows expression of human WISP-2 RNA in mesenchymal cells involved in tissue repair and/or collagen deposition. The signal was particularly strong in benign fibroblast-like cells adjacent to either infiltrating breast carcinoma cells or tissue destruction due to benign, inflammatory conditions (duct rupture). Of note is the fact that deposition of benign osteoid seemed to correlate with strong expression of the RNA.

(5) Human WISP-3

Expression in Normal Adult and Fetal Tissues and in Human Breast Carcinoma and Normal Breast Tissue and in Colon Carcinoma

The analysis shows strong expression of human WISP-3 in dermal fibroblasts in normal adult skin and in cirrhotic livers at sites of active hepatic fibrosis. This localization pattern supports a role for this growth factor in extracellular matrix formation and turnover.

The probe for human WISP-3 was negative on most tissues examined it showed a weak, diffuse positivity on sections of an osteosarcoma; some of the positive cells do represent malignant cells. WISP-3 was negative on all normal and fetal tissues examined.

Example 17 Ability of WISP Polypeptides to Inhibit VEGF-Stimulated Proliferation of Endothelial Cell Growth

The ability of mouse and human WISP-1 and human WISP-2 polypeptides to inhibit VEGF-stimulated proliferation of endothelial cells was tested. Specifically, bovine adrenal cortical capillary endothelial (ACE) cells (from primary culture, maximum 12-14 passages) were plated on 96-well microtiter plates (Amersham Life Science) at a density of 500 cells/well per 100 μL in low-glucose DMEM, 10% calf serum, 2 mM glutamine, 1× pen/strept, and flingizone, supplemented with 3 ng/mL VEGF. Controls were plated the same way but some did not include VEGF. A test sample of either mouse WISP-1, human WISP-1 conjugated to IgG, or human WISP-2 (PR0261) conjugated to poly-His was added in a 100-μl volume for a 200-μL final volume. Cells were incubated for 5-7 days at 37° C. The media were aspirated and the cells washed 1× with PBS. An acid phosphatase reaction mixture (100 μL, 0.1 M sodium acetate, pH 5.5, 0.1% TRITON-100™, 10 mM p-nitrophenyl phosphate) was added. After incubation for 2 hours at 37° C., the reaction was stopped by addition of 10 μl, 1 N NaOH. OD was measured on a microtiter plate reader at 405 mn. Controls were: no cells, cells alone, cells+FGF (5 ng/mL), cells+VEGF (3 ng/mL), cells+VEGF (3 ng/ml)+TGF-β (1 ng/ml), and cells+VEGF (3 ng/mL)+LIF (5 ng/mL) (TGF-β at a 1 ng/ml concentration is known to block 70-90% of VEGF-stimulated cell proliferation.)

The results were assessed by calculating the percentage inhibition of VEGF(3ng/ml)-stimulated cell proliferation, determined by measuring acid phosphatase activity at OD405 nm (1) relative to cells without stimulation, and (2) relative to the reference TGF-β inhibition of VEGF-stimulated activity. The results, as shown in Table X below, are indicative of the utility of the WISP polypeptides in cancer therapy and specifically in inhibiting tumor angiogenesis. The numerical values (relative inhibition) shown in Table x are determined by calculating the percent inhibition of VEGF-stimulated proliferation by the mouse WISP-1, human WISP-1-IgG, and human WISP-2-poly-His polypeptides relative to cells without stimulation and then dividing that percentage into the percent inhibition obtained by TGF-β at 1 ng/ml, which is known to block 70-90% of VEGF-stimulated cell proliferation. Human WISP-1 and human WISP-2 appear to be particularly useful as angiostatic agents. TABLE X Polypeptide Concentration (nM) Relative Inhibition Mouse WISP-1 0.1 113 ″ 1.0 108 ″ 10.0 109 Human WISP-1-IgG 1.1 1 ″ 11.0 0.95 ″ 110.0 0.9 Human WisP-2-poly-His 0.01 0.95 ″ 0.01% 1.1 ″ 0.1 0.62 ″ 1.0 1.03 ″ 1.0 0.5 ″ 1.0 0.6 Deposit of Material

The following materials have been deposited with the American Type Culture Collection, 10801 University Blvd., Manassas, Va., USA (ATCC): Material ATCC Dep. No. Deposit Date pRK5E.h.WIG-1.568.38 209533 Dec. 10, 1997 pRK5E.m.WIG-1.568.6his 209537 Dec. 10, 1997 Plasmid 209391 Oct. 17, 1997 (encoding human WISP-2) pRKE.m.WIG-2.1367.3 209538 Dec. 10, 1997 DNA56350-1176-2 209706 Mar. 26, 1998 DNA58800-1176-2 209707 Mar. 26, 1998

These deposits were made under the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purpose of Patent Procedure and the Regulations thereunder (Budapest Treaty). This assures maintenance of viable cultures of the deposits for 30 years from the date of deposit. The deposits will be made available by ATCC under the terms of the Budapest Treaty, and subject to an agreement between Genentech, Inc. and ATCC, which assures permanent and unrestricted availability of the progeny of the cultures of the deposits to the public upon issuance of the pertinent U.S. patent or upon laying open to the public of any U.S. or foreign patent application, whichever comes first, and assures availability of the progeny to one determined by the U.S. Commissioner of Patents and Trademarks to be entitled thereto according to 35 USC §122 and the Commissioner's rules pursuant thereto (including 37 CFR §1.14 with particular reference to 886 OG 638).

The assignee of the present application has agreed that if a culture of the materials on deposit should die or be lost or destroyed when cultivated under suitable conditions, the materials will be promptly replaced on notification with another of the same. Availability of the deposited materials is not to be construed as a license to practice the invention in contravention of the rights granted under the authority of any government in accordance with its patent laws.

The foregoing written specification is considered to be sufficient to enable one skilled in the art to practice the invention. The present invention is not to be limited in scope by the constructs deposited, since the deposited embodiment is intended as a single illustration of certain aspects of the invention and any constructs that are functionally equivalent are within the scope of this invention. The deposits of materials herein do not constitute an admission that the written description herein contained is inadequate to enable the practice of any aspect of the invention, including the best mode thereof, nor is it to be construed as limiting the scope of the claims to the specific illustrations that it represents. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and fall within the scope of the appended claims. 

1.-11. (canceled)
 12. A method for inhibiting the growth of tumor cells comprising exposing a cell that overexpresses a Wnt-1-induced gene to an effective amount of an antagonist that inhibits the expression or activity of a WISP-1 polypeptide.
 13. The method of claim 12 wherein said antagonist is an antibody specifically binding a WISP-1 polypeptide.
 14. The method of claim 12 or claim 13 wherein the tumor cells are colon cancer cells, the antibody is against human WISP-1 and is a humanized or human monoclonal antibody, and the tumor cells are those of a human. 